From 5270954497b2d4044b095903084216053b24516c Mon Sep 17 00:00:00 2001 From: github-actions Date: Wed, 12 Jun 2024 03:24:30 +0000 Subject: [PATCH] Updated the data.yml sourced from australianbiocommons.github.io --- _data/data.yaml | 11946 +++++++++++++++++++++++++++++++--------------- 1 file changed, 8069 insertions(+), 3877 deletions(-) diff --git a/_data/data.yaml b/_data/data.yaml index ab29a9a..8d5faa4 100644 --- a/_data/data.yaml +++ b/_data/data.yaml @@ -1,8 +1,23 @@ - biocontainers: 3d-dna + biotools: 3d-dna bunya: - '201008' description: 3D de novo assembly (3D-DNA) is a pipeline for de novo assembly using HiC. + edam-operations: + - term: Scaffolding + url: http://edamontology.org/operation_3216 + - term: De-novo assembly + url: http://edamontology.org/operation_0524 + - term: Genome assembly + url: http://edamontology.org/operation_0525 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Mapping + url: http://edamontology.org/topic_0102 + - term: DNA + url: http://edamontology.org/topic_0654 galaxy: '' homepage: https://github.com/aidenlab/3d-dna id: 3d-dna @@ -15,18 +30,23 @@ - title: De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds url: https://doi.org/10.1126/science.aal3327 - registry-link: 3d-dna - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - Mapping - - DNA + resources: + - title: .nan + url: .nan - biocontainers: ABRicate + biotools: ABRicate bunya: - 1.0.0-gompi-2021a description: Mass screening of contigs for antimicrobial resistance or virulence genes. + edam-operations: + - term: Antimicrobial resistance prediction + url: http://edamontology.org/operation_3482 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Microbiology + url: http://edamontology.org/topic_3301 galaxy: - description: 'ABRicate List: List all of abricate''s available databases.' title: ABRicate List 1.0.1 @@ -47,15 +67,23 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: ABRicate - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Microbiology + resources: + - title: .nan + url: .nan - biocontainers: abyss + biotools: abyss bunya: '' description: De novo genome sequence assembler using short reads. + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: De-novo assembly + url: http://edamontology.org/operation_0524 + - term: Scaffolding + url: http://edamontology.org/operation_3216 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: - description: 'ABySS: de novo sequence assembler' title: ABySS 2.3.7+galaxy0 @@ -73,18 +101,25 @@ url: https://doi.org/10.1101/gr.089532.108 - title: 10.1101/gr.214346.116 url: https://doi.org/10.1101/gr.214346.116 - registry-link: abyss - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly + resources: + - title: .nan + url: .nan - biocontainers: amber + biotools: amber bunya: '' description: 'The Assisted Model Building with Energy Refinement tool refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.' + edam-operations: + - term: Modelling and simulation + url: http://edamontology.org/operation_2426 + edam-topics: + - term: Molecular modelling + url: http://edamontology.org/topic_2275 + - term: Computational biology + url: http://edamontology.org/topic_3307 galaxy: - description: 'Generate MD topologies for small molecules: using acpype' title: Generate MD topologies for small molecules 21.10+galaxy0 @@ -105,18 +140,24 @@ url: https://doi.org/10.1002/jcc.20290 - title: An overview of the Amber biomolecular simulation package url: https://doi.org/10.1002/wcms.1121 - registry-link: amber - resource-description: .nan - resource-documentation: .nan - topics: - - Molecular modelling - - Computational biology + resources: + - title: .nan + url: .nan - biocontainers: ambertools + biotools: ambertools bunya: '' description: Consists of several independently developed packages that work well by themselves, and with Amber (Assisted Model Building with Energy Refinement) itself. The suite can also be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB), with generalized Born solvent models. + edam-operations: + - term: Molecular dynamics simulation + url: http://edamontology.org/operation_2476 + edam-topics: + - term: Molecular modelling + url: http://edamontology.org/topic_2275 + - term: Molecular dynamics + url: http://edamontology.org/topic_0176 galaxy: - description: 'MMPBSA/MMGBSA: tool for estimating ligand binding affinities' title: MMPBSA/MMGBSA 21.10+galaxy0 @@ -131,13 +172,11 @@ publications: - title: The Amber biomolecular simulation programs url: http://www.ncbi.nlm.nih.gov/pubmed/16200636 - registry-link: ambertools - resource-description: .nan - resource-documentation: .nan - topics: - - Molecular modelling - - Molecular dynamics + resources: + - title: .nan + url: .nan - biocontainers: anaconda + biotools: anaconda bunya: - '2022.05' description: "Software package specially developed for the study of genes\u2019\ @@ -145,6 +184,18 @@ \ as FASTA and GenBank, and it applies a set of statistical and visualization\ \ methods in different ways, to reveal information about codon context, codon\ \ usage, nucleotide repeats within open reading frames (ORFeome) and others." + edam-operations: + - term: Statistical inference + url: http://edamontology.org/operation_3658 + - term: Nucleic acid sequence analysis + url: http://edamontology.org/operation_2478 + - term: Coding region prediction + url: http://edamontology.org/operation_0436 + edam-topics: + - term: DNA + url: http://edamontology.org/topic_0654 + - term: Gene expression + url: http://edamontology.org/topic_0203 galaxy: '' homepage: http://bioinformatics.ua.pt/software/anaconda/ id: anaconda @@ -157,15 +208,15 @@ - title: Statistical, computational and visualization methodologies to unveil gene primary structure features url: http://www.ncbi.nlm.nih.gov/pubmed/16538282 - registry-link: anaconda - resource-description: .nan - resource-documentation: .nan - topics: - - DNA - - Gene expression + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Export AnnData and loom files: Interconvert AnnData and Loom formats' title: Export AnnData and loom files 0.10.3+galaxy0 @@ -187,11 +238,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: annotatemyids + biotools: annotatemyids bunya: '' description: This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly @@ -199,6 +250,10 @@ using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. + edam-operations: + - term: Annotation + url: http://edamontology.org/operation_0226 + edam-topics: '' galaxy: - description: 'annotateMyIDs: annotate a generic set of identifiers' title: annotateMyIDs 3.18.0+galaxy0 @@ -211,16 +266,28 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: annotatemyids - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: antismash + biotools: antismash bunya: '' description: Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. + edam-operations: + - term: Sequence clustering + url: http://edamontology.org/operation_0291 + - term: Gene prediction + url: http://edamontology.org/operation_2454 + - term: Differential gene expression analysis + url: http://edamontology.org/operation_3223 + edam-topics: + - term: Molecular interactions, pathways and networks + url: http://edamontology.org/topic_0602 + - term: Gene and protein families + url: http://edamontology.org/topic_0623 galaxy: - description: 'Antismash: allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters' @@ -244,16 +311,24 @@ url: https://doi.org/10.1093/NAR/GKX319 - title: 10.1093/NAR/GKAA978 url: https://doi.org/10.1093/NAR/GKAA978 - registry-link: antismash - resource-description: .nan - resource-documentation: .nan - topics: - - Molecular interactions, pathways and networks - - Gene and protein families + resources: + - title: .nan + url: .nan - biocontainers: any2fasta + biotools: any2fasta bunya: - 0.4.2-gcccore-10.3.0 description: Convert various sequence formats to FASTA + edam-operations: + - term: Formatting + url: http://edamontology.org/operation_0335 + - term: Sequence conversion + url: http://edamontology.org/operation_0233 + edam-topics: + - term: Data quality management + url: http://edamontology.org/topic_3572 + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: '' homepage: https://github.com/tseemann/any2fasta id: any2fasta @@ -263,17 +338,33 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: any2fasta - resource-description: .nan - resource-documentation: .nan - topics: - - Data quality management - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: apollo + biotools: apollo bunya: '' description: Apollo is a genome annotation viewer and editor. Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical environment. + edam-operations: + - term: Editing + url: http://edamontology.org/operation_3096 + - term: Sequence annotation + url: http://edamontology.org/operation_0361 + - term: Genome annotation + url: http://edamontology.org/operation_0362 + edam-topics: + - term: Data submission, annotation and curation + url: http://edamontology.org/topic_0219 + - term: Gene transcripts + url: http://edamontology.org/topic_3512 + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Mapping + url: http://edamontology.org/topic_0102 + - term: Molecular interactions, pathways and networks + url: http://edamontology.org/topic_0602 galaxy: '' homepage: http://apollo.berkeleybop.org id: apollo @@ -285,18 +376,21 @@ publications: - title: 'Apollo: a sequence annotation editor.' url: http://www.ncbi.nlm.nih.gov/pubmed/12537571 - registry-link: apollo - resource-description: Apollo Portal - resource-documentation: https://apollo-portal.genome.edu.au/ - topics: - - Data submission, annotation and curation - - Gene transcripts - - Genomics - - Mapping - - Molecular interactions, pathways and networks + resources: + - title: Apollo Portal + url: https://apollo-portal.genome.edu.au/ - biocontainers: aragorn + biotools: aragorn bunya: '' description: ARAGORN detects tRNA, mtRNA info about tmRNA, and tmRNA genes + edam-operations: + - term: Gene prediction + url: http://edamontology.org/operation_2454 + edam-topics: + - term: Functional, regulatory and non-coding RNA + url: http://edamontology.org/topic_0659 + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: - description: 'tRNA and tmRNA: prediction (Aragorn)' title: tRNA and tmRNA 0.6 @@ -311,15 +405,15 @@ publications: - title: ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences url: https://doi.org/10.1093/nar/gkh152 - registry-link: aragorn - resource-description: .nan - resource-documentation: .nan - topics: - - Functional, regulatory and non-coding RNA - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: argtable @@ -330,16 +424,28 @@ - '2.13' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: Arriba + biotools: Arriba bunya: '' description: Arriba is a command-line tool to detect gene fusions from RNA-Seq data based on the STAR aligner. In addition to fusions, it can detect exon duplications/inversions and truncations of genes (i.e., breakpoints in introns and intergenic regions). Arriba is the winner of the DREAM SMC-RNA Challenge. + edam-operations: + - term: Structural variation detection + url: http://edamontology.org/operation_3228 + - term: Split read mapping + url: http://edamontology.org/operation_3199 + edam-topics: + - term: Gene transcripts + url: http://edamontology.org/topic_3512 + - term: RNA splicing + url: http://edamontology.org/topic_3320 + - term: DNA structural variation + url: http://edamontology.org/topic_3175 galaxy: - description: 'Arriba: detect gene fusions from STAR aligned RNA-Seq data' title: Arriba 2.4.0+galaxy1 @@ -358,14 +464,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: Arriba - resource-description: .nan - resource-documentation: .nan - topics: - - Gene transcripts - - RNA splicing - - DNA structural variation + resources: + - title: .nan + url: .nan - biocontainers: augustus + biotools: augustus bunya: - 3.4.0-foss-2021a - 3.5.0-foss-2022a (D) @@ -374,6 +477,14 @@ PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. + edam-operations: + - term: Gene prediction + url: http://edamontology.org/operation_2454 + edam-topics: + - term: Gene transcripts + url: http://edamontology.org/topic_3512 + - term: Gene and protein families + url: http://edamontology.org/topic_0623 galaxy: - description: 'Augustus: gene prediction for prokaryotic and eukaryotic genomes' title: Augustus 3.4.0+galaxy1 @@ -388,6 +499,7 @@ nci-gadi: '' nci-if89: - 3.4.0 + - 3.5.0 pawsey: '' publications: - title: Gene prediction with a hidden Markov model and a new intron submodel @@ -411,17 +523,25 @@ url: https://doi.org/10.1007/978-1-4939-9173-0_5 - title: Multi-genome annotation with AUGUSTUS url: https://doi.org/10.1007/978-1-4939-9173-0_8 - registry-link: augustus - resource-description: .nan - resource-documentation: .nan - topics: - - Gene transcripts - - Gene and protein families + resources: + - title: .nan + url: .nan - biocontainers: autodock_vina + biotools: autodock_vina bunya: '' description: AutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use. + edam-operations: + - term: Molecular docking + url: http://edamontology.org/operation_0478 + edam-topics: + - term: Drug discovery + url: http://edamontology.org/topic_3336 + - term: Molecular modelling + url: http://edamontology.org/topic_2275 + - term: Molecular docking + url: http://edamontology.org/topic_2275 galaxy: - description: 'Prepare ligand: for docking with Autodock Vina' title: Prepare ligand 1.5.7+galaxy0 @@ -448,16 +568,23 @@ publications: - title: 10.1002/jcc.21334 url: https://doi.org/10.1002/jcc.21334 - registry-link: autodock_vina - resource-description: .nan - resource-documentation: .nan - topics: - - Drug discovery - - Molecular modelling - - Molecular docking + resources: + - title: .nan + url: .nan - biocontainers: bakta + biotools: bakta bunya: '' description: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids + edam-operations: + - term: Genome annotation + url: http://edamontology.org/operation_0362 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Data submission, annotation and curation + url: http://edamontology.org/topic_0219 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'Bakta: Genome annotation via alignment-free sequence identification' title: Bakta 1.9.2+galaxy0 @@ -472,19 +599,28 @@ publications: - title: 10.1099/mgen.0.000685 url: https://doi.org/10.1099/mgen.0.000685 - registry-link: bakta - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Data submission, annotation and curation - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: bamtools + biotools: bamtools bunya: - 2.5.2-gcc-10.3.0 - 2.5.2-gcc-11.3.0 (D) description: BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + - term: Sequence alignment analysis + url: http://edamontology.org/operation_0258 + edam-topics: + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Data management + url: http://edamontology.org/topic_3071 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'Split BAM by read tag value: into a dataset list collection' title: Split BAM by read tag value 2.5.2+galaxy2 @@ -507,16 +643,19 @@ publications: - title: 'Bamtools: A C++ API and toolkit for analyzing and managing BAM files' url: http://www.ncbi.nlm.nih.gov/pubmed/21493652 - registry-link: bamtools - resource-description: .nan - resource-documentation: .nan - topics: - - Sequencing - - Data management - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: bamutil + biotools: bamutil bunya: '' description: Bamutil provides a serie of programs to work on SAM/BAM files. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + edam-topics: + - term: Data management + url: http://edamontology.org/topic_3071 galaxy: - description: 'BamUtil diff: two coordinate sorted SAM/BAM files' title: BamUtil diff 1.0.15+galaxy1 @@ -532,16 +671,23 @@ - title: An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data url: https://doi.org/10.1101/gr.176552.114 - registry-link: bamutil - resource-description: .nan - resource-documentation: .nan - topics: - - Data management + resources: + - title: .nan + url: .nan - biocontainers: bandage + biotools: bandage bunya: '' description: GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. + edam-operations: + - term: Sequence assembly visualisation + url: http://edamontology.org/operation_3184 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: - description: 'Bandage Info: determine statistics of de novo assembly graphs' title: Bandage Info 2022.09+galaxy2 @@ -559,17 +705,25 @@ publications: - title: 10.1093/bioinformatics/btv383 url: https://doi.org/10.1093/bioinformatics/btv383 - registry-link: bandage - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Sequence assembly + resources: + - title: .nan + url: .nan - biocontainers: barrnap + biotools: barrnap bunya: '' description: Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). + edam-operations: + - term: Gene prediction + url: http://edamontology.org/operation_2454 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Model organisms + url: http://edamontology.org/topic_0621 + - term: Model organisms + url: http://edamontology.org/topic_0621 galaxy: - description: 'barrnap: Locate ribosomal RNA''s in a fasta file. (GFF output)' title: barrnap 1.2.2 @@ -582,17 +736,16 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: barrnap - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Model organisms - - Model organisms + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 1.5.3 matlab description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: basespace @@ -602,21 +755,47 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: bbmap + biotools: bbmap bunya: - 38.96-gcc-10.3.0 - 39.01-gcc-11.3.0 (D) description: BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. + edam-operations: + - term: RNA-Seq analysis + url: http://edamontology.org/operation_3680 + - term: Sequence trimming + url: http://edamontology.org/operation_3192 + - term: Read mapping + url: http://edamontology.org/operation_3198 + - term: Sequence contamination filtering + url: http://edamontology.org/operation_3187 + - term: Read binning + url: http://edamontology.org/operation_3798 + - term: Sequence alignment + url: http://edamontology.org/operation_0292 + edam-topics: + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: RNA splicing + url: http://edamontology.org/topic_3320 + - term: Whole genome sequencing + url: http://edamontology.org/topic_3673 + - term: Phylogenetics + url: http://edamontology.org/topic_3293 + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: RNA-Seq + url: http://edamontology.org/topic_3170 galaxy: - description: 'BBTools: BBduk: decontamination using kmers' - title: 'BBTools: BBduk 39.06+galaxy0' - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbbtools_bbduk%2Fbbtools_bbduk%2F39.06%2Bgalaxy0 + title: 'BBTools: BBduk 39.06+galaxy2' + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbbtools_bbduk%2Fbbtools_bbduk%2F39.06%2Bgalaxy2 homepage: https://jgi.doe.gov/data-and-tools/bbtools/ id: bbmap license: BSD-3-Clause @@ -627,21 +806,21 @@ pawsey: - 38.96--h5c4e2a8_0 publications: '' - registry-link: bbmap - resource-description: .nan - resource-documentation: .nan - topics: - - Sequencing - - RNA splicing - - Whole genome sequencing - - Phylogenetics - - Metagenomics - - RNA-Seq + resources: + - title: .nan + url: .nan - biocontainers: gff3_rebase + biotools: gff3_rebase bunya: '' description: A tool for filling the gap created by genomic data processing/analysis by rebasing some analysis results against the parent features which were originally analysed. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + - term: Formatting + url: http://edamontology.org/operation_0335 + edam-topics: '' galaxy: - description: 'Rebase GFF3 features: against parent features' title: Rebase GFF3 features 1.2 @@ -663,17 +842,31 @@ - title: 'Biopython: Freely available Python tools for computational molecular biology and bioinformatics' url: https://doi.org/10.1093/bioinformatics/btp163 - registry-link: gff3_rebase - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: bcftools + biotools: bcftools bunya: - 1.12-gcc-10.3.0 - 1.15.1-gcc-11.3.0 (D) description: BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + - term: Variant calling + url: http://edamontology.org/operation_3227 + edam-topics: + - term: Genetic variation + url: http://edamontology.org/topic_0199 + - term: DNA polymorphism + url: http://edamontology.org/topic_2885 + - term: GWAS study + url: http://edamontology.org/topic_3517 + - term: Genotyping experiment + url: http://edamontology.org/topic_3516 galaxy: - description: 'bcftools annotate: Annotate and edit VCF/BCF files' title: bcftools annotate 1.15.1+galaxy3 @@ -796,18 +989,16 @@ url: https://doi.org/10.1093/bioinformatics/btp352 - title: Twelve years of SAMtools and BCFtools url: https://doi.org/10.1093/gigascience/giab008 - registry-link: bcftools - resource-description: .nan - resource-documentation: .nan - topics: - - Genetic variation - - DNA polymorphism - - GWAS study - - Genotyping experiment + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 2.20.0-gcc-11.3.0 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: bcl2fastq2 @@ -817,15 +1008,23 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: beagle + biotools: beagle bunya: - 5.4.22jul22.46e-java-11 description: Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection. + edam-operations: + - term: Phasing + url: http://edamontology.org/operation_3454 + - term: Imputation + url: http://edamontology.org/operation_3557 + edam-topics: + - term: Population genetics + url: http://edamontology.org/topic_3056 galaxy: '' homepage: https://faculty.washington.edu/browning/beagle/beagle.html id: beagle @@ -844,17 +1043,28 @@ url: https://doi.org/10.1016/j.ajhg.2021.08.005 - title: A One-Penny Imputed Genome from Next-Generation Reference Panels url: https://doi.org/10.1016/j.ajhg.2018.07.015 - registry-link: beagle - resource-description: .nan - resource-documentation: .nan - topics: - - Population genetics + resources: + - title: .nan + url: .nan - biocontainers: beagle-lib + biotools: beagle-lib bunya: - 3.1.2-gcc-11.3.0 - 4.0.0-gcc-11.3.0 (D) description: BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. + edam-operations: + - term: Phylogenetic inference + url: http://edamontology.org/operation_0323 + - term: Standardisation and normalisation + url: http://edamontology.org/operation_3435 + edam-topics: + - term: Phylogenetics + url: http://edamontology.org/topic_3293 + - term: Statistics and probability + url: http://edamontology.org/topic_2269 + - term: Computer science + url: http://edamontology.org/topic_3316 galaxy: '' homepage: https://github.com/beagle-dev/beagle-lib id: beagle-lib @@ -868,14 +1078,11 @@ - title: 'BEAGLE: An application programming interface and high-performance computing library for statistical phylogenetics' url: https://doi.org/10.1093/sysbio/syr100 - registry-link: beagle-lib - resource-description: .nan - resource-documentation: .nan - topics: - - Phylogenetics - - Statistics and probability - - Computer science + resources: + - title: .nan + url: .nan - biocontainers: beast + biotools: beast bunya: '' description: The Bayesian Evolutionary Analysis Sampling Trees is a cross-platform program for Bayesian analysis of molecular sequences using MCMC (Markov chain @@ -883,6 +1090,18 @@ inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. + edam-operations: + - term: Multiple sequence alignment + url: http://edamontology.org/operation_0492 + - term: Phylogenetic tree generation (from molecular sequences) + url: http://edamontology.org/operation_0540 + - term: Phylogenetic tree generation (maximum likelihood and Bayesian methods) + url: http://edamontology.org/operation_0547 + edam-topics: + - term: Phylogenetics + url: http://edamontology.org/topic_3293 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: '' homepage: http://beast.bio.ed.ac.uk/ id: beast @@ -900,13 +1119,11 @@ url: https://doi.org/10.1093/ve/vey016 - title: 'BEAST: Bayesian evolutionary analysis by sampling trees' url: https://doi.org/10.1186/1471-2148-7-214 - registry-link: beast - resource-description: .nan - resource-documentation: .nan - topics: - - Phylogenetics - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: beast2 + biotools: beast2 bunya: '' description: Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. @@ -916,6 +1133,16 @@ tree is weighted proportional to its posterior probability. It includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results. + edam-operations: + - term: Phylogenetic tree reconstruction + url: http://edamontology.org/operation_3478 + - term: Phylogenetic tree analysis (shape) + url: http://edamontology.org/operation_0551 + edam-topics: + - term: Phylogenetics + url: http://edamontology.org/topic_3293 + - term: Phylogenomics + url: http://edamontology.org/topic_0194 galaxy: '' homepage: http://www.beast2.org id: beast2 @@ -928,16 +1155,20 @@ publications: - title: 'BEAST 2: A Software Platform for Bayesian Evolutionary Analysis' url: https://doi.org/10.1371/JOURNAL.PCBI.1003537 - registry-link: beast2 - resource-description: .nan - resource-documentation: .nan - topics: - - Phylogenetics - - Phylogenomics + resources: + - title: .nan + url: .nan - biocontainers: bed_to_protein_map + biotools: bed_to_protein_map bunya: '' description: Convert a BED format file of the proteins from a proteomics search database into a tabular format for the Multiomics Visualization Platform (MVP). + edam-operations: + - term: Conversion + url: http://edamontology.org/operation_3434 + edam-topics: + - term: Literature and language + url: http://edamontology.org/topic_3068 galaxy: - description: 'bed to protein map: genomic location of proteins for MVP' title: bed to protein map 0.2.0 @@ -950,14 +1181,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: bed_to_protein_map - resource-description: .nan - resource-documentation: .nan - topics: - - Literature and language + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'BED-to-GFF: converter' title: BED-to-GFF 2.0.0 @@ -970,16 +1202,22 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: bedtools + biotools: bedtools bunya: - 2.30.0-gcc-10.3.0 - 2.30.0-gcc-11.3.0 (D) description: BEDTools is an extensive suite of utilities for comparing genomic features in BED format. + edam-operations: + - term: Mapping + url: http://edamontology.org/operation_2429 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: - description: 'bedtools GroupByBed: group by common cols and summarize other cols' title: bedtools GroupByBed 2.30.0 @@ -1130,12 +1368,11 @@ publications: - title: 'BEDTools: A flexible suite of utilities for comparing genomic features' url: http://www.ncbi.nlm.nih.gov/pubmed/20110278 - registry-link: bedtools - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: Bellerophon + biotools: Bellerophon bunya: '' description: 'The Bellerophon pipeline, improving de novo transcriptomes and removing chimeras. @@ -1147,6 +1384,26 @@ The pipeline can be downloaded as a vragrant virtual machine (https://app.vagrantup.com/bellerophon/boxes/bellerophon). This is recommended, as it avoids backwards compatibility problems with TransRate' + edam-operations: + - term: De-novo assembly + url: http://edamontology.org/operation_0524 + - term: Validation + url: http://edamontology.org/operation_2428 + - term: de Novo sequencing + url: http://edamontology.org/operation_3644 + - term: Transcriptome assembly + url: http://edamontology.org/operation_3258 + - term: Chimera detection + url: http://edamontology.org/operation_0450 + edam-topics: + - term: Transcriptomics + url: http://edamontology.org/topic_3308 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: RNA-Seq + url: http://edamontology.org/topic_3170 + - term: Workflows + url: http://edamontology.org/topic_0769 galaxy: - description: 'Filter and merge: chimeric reads from Arima Genomics' title: Filter and merge 1.0+galaxy1 @@ -1162,17 +1419,21 @@ - title: The Bellerophon pipeline, improving de novo transcriptomes and removing chimeras url: https://doi.org/10.1002/ECE3.5571 - registry-link: Bellerophon - resource-description: .nan - resource-documentation: .nan - topics: - - Transcriptomics - - Sequence assembly - - RNA-Seq - - Workflows + resources: + - title: .nan + url: .nan - biocontainers: berokka + biotools: berokka bunya: '' description: Trim, circularise, orient and filter long read bacterial genome assemblies + edam-operations: + - term: Filtering + url: http://edamontology.org/operation_3695 + - term: Sequence trimming + url: http://edamontology.org/operation_3192 + edam-topics: + - term: Computer science + url: http://edamontology.org/topic_3316 galaxy: - description: 'Berokka: Trim, circularise, orient and filter long read bacterial genome assemblies' @@ -1186,14 +1447,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: berokka - resource-description: .nan - resource-documentation: .nan - topics: - - Computer science + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Convert image format: with Bioformats' title: Convert image format 6.7.0+galaxy2 @@ -1209,15 +1471,17 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 1.7.3-gcc-10.3.0 - 1.7.3-gcc-11.3.0 (D) description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: bio-searchio-hmmer @@ -1227,14 +1491,32 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: bio3d + biotools: bio3d bunya: '' description: Bio3D is an R package containing utilities for the analysis of protein structure, sequence and trajectory data. + edam-operations: + - term: Essential dynamics + url: http://edamontology.org/operation_3891 + - term: Molecular dynamics + url: http://edamontology.org/operation_2476 + - term: Protein structure analysis + url: http://edamontology.org/operation_2406 + - term: Principal component visualisation + url: http://edamontology.org/operation_2939 + - term: Sequence trimming + url: http://edamontology.org/operation_3192 + edam-topics: + - term: Structure analysis + url: http://edamontology.org/topic_0081 + - term: Gene and protein families + url: http://edamontology.org/topic_0623 + - term: Bioinformatics + url: http://edamontology.org/topic_0091 galaxy: - description: 'PCA: - principal component analysis using Bio3D' title: PCA 2.3.4 @@ -1259,17 +1541,16 @@ publications: - title: The Bio3D packages for structural bioinformatics url: https://doi.org/10.1002/PRO.3923 - registry-link: bio3d - resource-description: .nan - resource-documentation: .nan - topics: - - Structure analysis - - Gene and protein families - - Bioinformatics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - '3.1' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: biobakery_workflows @@ -1279,14 +1560,20 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: biobambam + biotools: biobambam bunya: '' description: Tools for early stage NGS alignment file processing including fast sorting and duplicate marking. + edam-operations: + - term: Filtering + url: http://edamontology.org/operation_3695 + edam-topics: + - term: Sequencing + url: http://edamontology.org/topic_3168 galaxy: '' homepage: http://www.sanger.ac.uk/science/tools/biobambam id: biobambam @@ -1299,15 +1586,16 @@ publications: - title: 'Biobambam: Tools for read pair collation based algorithms on BAM files' url: https://doi.org/10.1186/1751-0473-9-13 - registry-link: biobambam - resource-description: .nan - resource-documentation: .nan - topics: - - Sequencing + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 3.01-gcc-11.3.0 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://github.com/Ensembl/Bio-DB-HTS id: bio-db-hts @@ -1317,11 +1605,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: biomformat + biotools: biomformat bunya: '' description: This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for @@ -1329,6 +1617,14 @@ to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods. + edam-operations: + - term: Formatting + url: http://edamontology.org/operation_0335 + edam-topics: + - term: Laboratory information management + url: http://edamontology.org/topic_0607 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'Convert: between BIOM table formats' title: Convert 2.1.15+galaxy1 @@ -1346,15 +1642,15 @@ publications: - title: Orchestrating high-throughput genomic analysis with Bioconductor url: https://doi.org/10.1038/nmeth.3252 - registry-link: biomformat - resource-description: .nan - resource-documentation: .nan - topics: - - Laboratory information management - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Bionano Hybrid Scaffold: automates the scaffolding process' title: Bionano Hybrid Scaffold 3.7.0+galaxy3 @@ -1367,17 +1663,29 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: bioperl + biotools: bioperl bunya: - 1.7.8-gcccore-10.3.0 - 1.7.8-gcccore-11.3.0 (D) description: A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + - term: Service invocation + url: http://edamontology.org/operation_3763 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Software engineering + url: http://edamontology.org/topic_3372 + - term: Data management + url: http://edamontology.org/topic_3071 galaxy: '' homepage: http://bioperl.org/ id: bioperl @@ -1389,19 +1697,34 @@ publications: - title: An introduction to BioPerl url: https://doi.org/10.1007/978-1-59745-535-0_26 - registry-link: bioperl - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Software engineering - - Data management + resources: + - title: .nan + url: .nan - biocontainers: biopython + biotools: biopython bunya: - 1.79-foss-2021a - 1.79-foss-2022a (D) description: Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. + edam-operations: + - term: Deposition + url: http://edamontology.org/operation_3431 + - term: Service invocation + url: http://edamontology.org/operation_3763 + - term: Query and retrieval + url: http://edamontology.org/operation_0224 + - term: Aggregation + url: http://edamontology.org/operation_3436 + edam-topics: + - term: Bioinformatics + url: http://edamontology.org/topic_0091 + - term: Data management + url: http://edamontology.org/topic_3071 + - term: Software engineering + url: http://edamontology.org/topic_3372 + - term: Computational biology + url: http://edamontology.org/topic_3307 galaxy: - description: 'Translate BED transcripts: cDNA in 3frames or CDS' title: Translate BED transcripts 0.1.0 @@ -1426,18 +1749,32 @@ - title: 'Biopython: Freely available Python tools for computational molecular biology and bioinformatics' url: http://www.ncbi.nlm.nih.gov/pubmed/19304878 - registry-link: biopython - resource-description: .nan - resource-documentation: .nan - topics: - - Bioinformatics - - Data management - - Software engineering - - Computational biology + resources: + - title: .nan + url: .nan - biocontainers: biotransformer + biotools: biotransformer bunya: '' description: BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. + edam-operations: + - term: Metabolic pathway prediction + url: http://edamontology.org/operation_3929 + - term: PTM site prediction + url: http://edamontology.org/operation_0417 + - term: Natural product identification + url: http://edamontology.org/operation_3803 + edam-topics: + - term: Small molecules + url: http://edamontology.org/topic_0154 + - term: Endocrinology and metabolism + url: http://edamontology.org/topic_3407 + - term: Metabolomics + url: http://edamontology.org/topic_3172 + - term: Carbohydrates + url: http://edamontology.org/topic_0152 + - term: NMR + url: http://edamontology.org/topic_0593 galaxy: - description: 'BioTransformer: ' title: BioTransformer 3.0_20230403+galaxy1 @@ -1453,22 +1790,74 @@ - title: BioTransformer 3.0 - a web server for accurately predicting metabolic transformation products url: https://doi.org/10.1093/NAR/GKAC313 - registry-link: biotransformer - resource-description: .nan - resource-documentation: .nan - topics: - - Small molecules - - Endocrinology and metabolism - - Metabolomics - - Carbohydrates - - NMR + resources: + - title: .nan + url: .nan +- biocontainers: bismark + biotools: bismark + bunya: '' + description: Bismark is a tool to map bisulfite treated sequencing reads and perform + methylation calling in a quick and easy-to-use fashion. + edam-operations: + - term: Methylation analysis + url: http://edamontology.org/operation_3204 + - term: Read mapping + url: http://edamontology.org/operation_3198 + - term: Bisulfite mapping + url: http://edamontology.org/operation_3186 + edam-topics: + - term: Epigenomics + url: http://edamontology.org/topic_3173 + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Epigenetics + url: http://edamontology.org/topic_3295 + galaxy: + - description: 'Bismark Deduplicate: Deduplicates reads mapped by Bismark' + title: Bismark Deduplicate 0.22.1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fbismark%2Fbismark_deduplicate%2F0.22.1 + - description: 'Bismark Pretty Report: Generates a graphical HTML report page from + report outputs of Bismark' + title: Bismark Pretty Report 0.22.1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fbismark%2Fbismark_pretty_report%2F0.22.1 + - description: 'Bismark Meth. Extractor: Reports on methylation status of reads + mapped by Bismark' + title: Bismark Meth. Extractor 0.22.1+galaxy1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fbismark%2Fbismark_methylation_extractor%2F0.22.1%2Bgalaxy1 + - description: 'Bismark Mapper: Bisulfite reads mapper' + title: Bismark Mapper 0.22.1+galaxy4 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fbismark%2Fbismark_bowtie2%2F0.22.1%2Bgalaxy4 + homepage: https://github.com/FelixKrueger/Bismark + id: bismark + license: GPL-3.0 + name: bismark + nci-gadi: '' + nci-if89: '' + pawsey: '' + publications: + - title: 'Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications' + url: http://www.ncbi.nlm.nih.gov/pubmed/21493656 + resources: + - title: .nan + url: .nan - biocontainers: blast + biotools: blast bunya: - 2.11.0-linux_x86_64 - 2.13.0--hf3cf87c_0 description: A tool that finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. + edam-operations: + - term: Sequence similarity search + url: http://edamontology.org/operation_0346 + - term: Sequence alignment + url: http://edamontology.org/operation_0292 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Bioinformatics + url: http://edamontology.org/topic_0091 galaxy: '' homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi id: blast @@ -1491,77 +1880,85 @@ url: https://doi.org/10.1093/nar/gkn201 - title: 'BLAST: a more efficient report with usability improvements.' url: https://doi.org/10.1093/nar/gkt282 - registry-link: blast - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis - - Bioinformatics + resources: + - title: .nan + url: .nan - biocontainers: blast + biotools: blast bunya: - 2.11.0-gompi-2021a - 2.13.0-gompi-2022a (D) description: A tool that finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. + edam-operations: + - term: Sequence similarity search + url: http://edamontology.org/operation_0346 + - term: Sequence alignment + url: http://edamontology.org/operation_0292 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Bioinformatics + url: http://edamontology.org/topic_0091 galaxy: - description: 'NCBI BLAST+ segmasker: low-complexity regions in protein sequences' - title: NCBI BLAST+ segmasker 2.14.1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_segmasker_wrapper%2F2.14.1%2Bgalaxy1 + title: NCBI BLAST+ segmasker 2.14.1+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_segmasker_wrapper%2F2.14.1%2Bgalaxy2 - description: 'NCBI BLAST+ convert2blastmask: Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb' - title: NCBI BLAST+ convert2blastmask 2.14.1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_convert2blastmask_wrapper%2F2.14.1%2Bgalaxy1 + title: NCBI BLAST+ convert2blastmask 2.14.1+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_convert2blastmask_wrapper%2F2.14.1%2Bgalaxy2 - description: 'NCBI BLAST+ makeblastdb: Make BLAST database' - title: NCBI BLAST+ makeblastdb 2.14.1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_makeblastdb%2F2.14.1%2Bgalaxy1 + title: NCBI BLAST+ makeblastdb 2.14.1+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_makeblastdb%2F2.14.1%2Bgalaxy2 - description: 'NCBI BLAST+ blastn: Search nucleotide database with nucleotide query sequence(s)' - title: NCBI BLAST+ blastn 2.14.1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_blastn_wrapper%2F2.14.1%2Bgalaxy1 + title: NCBI BLAST+ blastn 2.14.1+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_blastn_wrapper%2F2.14.1%2Bgalaxy2 - description: 'NCBI BLAST+ tblastx: Search translated nucleotide database with translated nucleotide query sequence(s)' - title: NCBI BLAST+ tblastx 2.14.1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_tblastx_wrapper%2F2.14.1%2Bgalaxy1 + title: NCBI BLAST+ tblastx 2.14.1+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_tblastx_wrapper%2F2.14.1%2Bgalaxy2 - description: 'NCBI BLAST+ tblastn: Search translated nucleotide database with protein query sequence(s)' - title: NCBI BLAST+ tblastn 2.14.1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_tblastn_wrapper%2F2.14.1%2Bgalaxy1 + title: NCBI BLAST+ tblastn 2.14.1+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_tblastn_wrapper%2F2.14.1%2Bgalaxy2 - description: 'BLAST XML to tabular: Convert BLAST XML output to tabular' - title: BLAST XML to tabular 2.14.1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fblastxml_to_tabular%2F2.14.1%2Bgalaxy1 + title: BLAST XML to tabular 2.14.1+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fblastxml_to_tabular%2F2.14.1%2Bgalaxy2 - description: 'NCBI get species taxids: ' - title: NCBI get species taxids 2.14.1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fget_species_taxids%2F2.14.1%2Bgalaxy1 + title: NCBI get species taxids 2.14.1+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fget_species_taxids%2F2.14.1%2Bgalaxy2 - description: 'NCBI BLAST+ rpstblastn: Search protein domain database (PSSMs) with translated nucleotide query sequence(s)' - title: NCBI BLAST+ rpstblastn 2.14.1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_rpstblastn_wrapper%2F2.14.1%2Bgalaxy1 + title: NCBI BLAST+ rpstblastn 2.14.1+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_rpstblastn_wrapper%2F2.14.1%2Bgalaxy2 - description: 'NCBI BLAST+ blastdbcmd entry(s): Extract sequence(s) from BLAST database' - title: NCBI BLAST+ blastdbcmd entry(s) 2.14.1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_blastdbcmd_wrapper%2F2.14.1%2Bgalaxy1 + title: NCBI BLAST+ blastdbcmd entry(s) 2.14.1+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_blastdbcmd_wrapper%2F2.14.1%2Bgalaxy2 - description: 'NCBI BLAST+ blastx: Search protein database with translated nucleotide query sequence(s)' - title: NCBI BLAST+ blastx 2.14.1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_blastx_wrapper%2F2.14.1%2Bgalaxy1 + title: NCBI BLAST+ blastx 2.14.1+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_blastx_wrapper%2F2.14.1%2Bgalaxy2 - description: 'NCBI BLAST+ dustmasker: masks low complexity regions' - title: NCBI BLAST+ dustmasker 2.14.1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_dustmasker_wrapper%2F2.14.1%2Bgalaxy1 + title: NCBI BLAST+ dustmasker 2.14.1+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_dustmasker_wrapper%2F2.14.1%2Bgalaxy2 - description: 'NCBI BLAST+ makeprofiledb: Make profile database' - title: NCBI BLAST+ makeprofiledb 2.14.1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_makeprofiledb%2F2.14.1%2Bgalaxy1 + title: NCBI BLAST+ makeprofiledb 2.14.1+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_makeprofiledb%2F2.14.1%2Bgalaxy2 - description: 'NCBI BLAST+ blastp: Search protein database with protein query sequence(s)' - title: NCBI BLAST+ blastp 2.14.1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_blastp_wrapper%2F2.14.1%2Bgalaxy1 + title: NCBI BLAST+ blastp 2.14.1+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_blastp_wrapper%2F2.14.1%2Bgalaxy2 - description: 'NCBI BLAST+ rpsblast: Search protein domain database (PSSMs) with protein query sequence(s)' - title: NCBI BLAST+ rpsblast 2.14.1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_rpsblast_wrapper%2F2.14.1%2Bgalaxy1 + title: NCBI BLAST+ rpsblast 2.14.1+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_rpsblast_wrapper%2F2.14.1%2Bgalaxy2 - description: 'NCBI BLAST+ database info: Show BLAST database information from blastdbcmd' - title: NCBI BLAST+ database info 2.14.1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_blastdbcmd_info%2F2.14.1%2Bgalaxy1 + title: NCBI BLAST+ database info 2.14.1+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fncbi_blast_plus%2Fncbi_blastdbcmd_info%2F2.14.1%2Bgalaxy2 homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi id: blast+ license: '' @@ -1578,16 +1975,20 @@ url: https://doi.org/10.1093/nar/gkn201 - title: 'BLAST: a more efficient report with usability improvements.' url: https://doi.org/10.1093/nar/gkt282 - registry-link: blast - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis - - Bioinformatics + resources: + - title: .nan + url: .nan - biocontainers: blat + biotools: blat bunya: - 3.7-gcc-11.3.0 description: Fast, accurate spliced alignment of DNA sequences. + edam-operations: + - term: Sequence alignment + url: http://edamontology.org/operation_0292 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: '' homepage: http://genome.ucsc.edu/cgi-bin/hgBlat?command=start id: blat @@ -1600,14 +2001,19 @@ publications: - title: BLAT - The BLAST-like alignment tool url: http://www.ncbi.nlm.nih.gov/pubmed/11932250 - registry-link: blat - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: blockbuster + biotools: blockbuster bunya: '' description: detect blocks of overlapping reads using a gaussian-distribution approach + edam-operations: + - term: RNA-Seq analysis + url: http://edamontology.org/operation_3680 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: - description: 'blockbuster: detects blocks of overlapping reads using a gaussian-distribution approach' @@ -1623,14 +2029,15 @@ publications: - title: Evidence for human microRNA-offset RNAs in small RNA sequencing data url: https://doi.org/10.1093/bioinformatics/btp419 - registry-link: blockbuster - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles' @@ -1644,14 +2051,16 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 2.4.1-intel-2022a description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://alkesgroup.broadinstitute.org/BOLT-LMM/BOLT-LMM_manual.html id: bolt-lmm @@ -1661,17 +2070,27 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: boost + biotools: boost bunya: - 1.76.0-gcc-10.3.0 - 1.79.0-gcc-11.3.0 (D) description: Boost is a set of libraries for the C++ programming language that provides support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading, image processing, regular expressions, and unit testing. + edam-operations: + - term: Image analysis + url: http://edamontology.org/operation_3443 + edam-topics: + - term: Pure mathematics + url: http://edamontology.org/topic_3570 + - term: Imaging + url: http://edamontology.org/topic_3382 + - term: Software engineering + url: http://edamontology.org/topic_3372 galaxy: '' homepage: https://www.boost.org/ id: boost @@ -1686,21 +2105,30 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: boost - resource-description: .nan - resource-documentation: .nan - topics: - - Pure mathematics - - Imaging - - Software engineering + resources: + - title: .nan + url: .nan - biocontainers: bowtie + biotools: bowtie bunya: - 1.3.1-gcc-11.3.0 description: Bowtie is an ultrafast, memory-efficient short read aligner. + edam-operations: + - term: Sequence alignment + url: http://edamontology.org/operation_0292 + edam-topics: + - term: Mapping + url: http://edamontology.org/topic_0102 + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: - description: 'Bowtie2: - map reads against reference genome' - title: Bowtie2 2.5.3+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fbowtie2%2Fbowtie2%2F2.5.3%2Bgalaxy0 + title: Bowtie2 2.5.3+galaxy1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fbowtie2%2Fbowtie2%2F2.5.3%2Bgalaxy1 - description: 'Map with Bowtie for Illumina: ' title: Map with Bowtie for Illumina 1.2.0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fbowtie_wrappers%2Fbowtie_wrapper%2F1.2.0 @@ -1719,15 +2147,11 @@ url: https://doi.org/10.1186/1471-2105-14-184 - title: 10.7490/f1000research.1114334.1 url: https://doi.org/10.7490/f1000research.1114334.1 - registry-link: bowtie - resource-description: .nan - resource-documentation: .nan - topics: - - Mapping - - Genomics - - Sequencing - - Sequence assembly + resources: + - title: .nan + url: .nan - biocontainers: bowtie2 + biotools: bowtie2 bunya: - 2.4.4-gcc-10.3.0 - 2.4.5-gcc-11.3.0 (D) @@ -1738,6 +2162,16 @@ an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.' + edam-operations: + - term: Read mapping + url: http://edamontology.org/operation_3198 + edam-topics: + - term: Mapping + url: http://edamontology.org/topic_0102 + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Mapping + url: http://edamontology.org/topic_0102 galaxy: '' homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml id: bowtie2 @@ -1763,16 +2197,15 @@ url: https://doi.org/10.1093/bioinformatics/btu146 - title: 10.7490/f1000research.1114334.1 url: https://doi.org/10.7490/f1000research.1114334.1 - registry-link: bowtie2 - resource-description: .nan - resource-documentation: .nan - topics: - - Mapping - - Genomics - - Mapping + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Genbank to GFF3: converter' title: Genbank to GFF3 1.1 @@ -1785,32 +2218,25 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' -- biocontainers: '' - bunya: '' - description: '' - galaxy: '' - homepage: '' - id: bq_radiomics - license: '' - name: bq_radiomics - nci-gadi: '' - nci-if89: - - 1.0.1 - pawsey: '' - publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: braker1 + biotools: braker1 bunya: - 3.0.3 description: Pipeline for unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS. + edam-operations: + - term: Genome annotation + url: http://edamontology.org/operation_0362 + edam-topics: + - term: RNA-Seq + url: http://edamontology.org/topic_3170 + - term: RNA + url: http://edamontology.org/topic_0099 + - term: Workflows + url: http://edamontology.org/topic_0769 galaxy: - description: 'BRAKER3: genome annotation' title: BRAKER3 3.0.6+galaxy2 @@ -1826,16 +2252,23 @@ - title: 'BRAKER1: Unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS' url: http://www.ncbi.nlm.nih.gov/pubmed/26559507 - registry-link: braker1 - resource-description: .nan - resource-documentation: .nan - topics: - - RNA-Seq - - RNA - - Workflows + resources: + - title: .nan + url: .nan - biocontainers: breseq + biotools: breseq bunya: '' description: Runs Breseq software on a set of fastq files. + edam-operations: + - term: Polymorphism detection + url: http://edamontology.org/operation_3202 + edam-topics: + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: DNA mutation + url: http://edamontology.org/topic_2533 galaxy: - description: 'breseq: find mutations in haploid microbial genomes' title: breseq 0.35.5+0 @@ -1856,20 +2289,35 @@ url: https://doi.org/10.1093/nar/gkw343 - title: 10.7490/f1000research.1114334.1 url: https://doi.org/10.7490/f1000research.1114334.1 - registry-link: breseq - resource-description: .nan - resource-documentation: .nan - topics: - - Sequencing - - Sequence analysis - - DNA mutation + resources: + - title: .nan + url: .nan - biocontainers: busco + biotools: busco bunya: - 5.4.2-foss-2021a - 5.4.5-foss-2022a (D) description: Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. + edam-operations: + - term: Sequence assembly validation + url: http://edamontology.org/operation_3180 + - term: Scaffolding + url: http://edamontology.org/operation_3216 + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: Transcriptome assembly + url: http://edamontology.org/operation_3258 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Transcriptomics + url: http://edamontology.org/topic_3308 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'Busco: assess genome assembly and annotation completeness' title: Busco 5.5.0+galaxy0 @@ -1892,17 +2340,29 @@ url: https://doi.org/10.1093/molbev/msx319 - title: 10.1093/molbev/msab199 url: https://doi.org/10.1093/molbev/msab199 - registry-link: busco - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - Genomics - - Transcriptomics - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: buttery_eel + biotools: buttery_eel bunya: '' description: Accelerated nanopore basecalling with SLOW5 data format. + edam-operations: + - term: Base-calling + url: http://edamontology.org/operation_3185 + - term: Formatting + url: http://edamontology.org/operation_0335 + - term: Splitting + url: http://edamontology.org/operation_3359 + edam-topics: + - term: Computer science + url: http://edamontology.org/topic_3316 + - term: Protein expression + url: http://edamontology.org/topic_0108 + - term: Workflows + url: http://edamontology.org/topic_0769 + - term: Transcription factors and regulatory sites + url: http://edamontology.org/topic_0749 galaxy: '' homepage: https://github.com/Psy-Fer/buttery-eel id: buttery-eel @@ -1912,24 +2372,28 @@ nci-if89: - 0.3.1+guppy6.4.2 - 0.4.1+guppy6.5.7 + - 0.4.2+dorado7.2.13 + - 0.4.2+guppy6.5.7 pawsey: '' publications: - title: Accelerated nanopore basecalling with SLOW5 data format url: https://doi.org/10.1093/BIOINFORMATICS/BTAD352 - registry-link: buttery_eel - resource-description: .nan - resource-documentation: .nan - topics: - - Computer science - - Protein expression - - Workflows - - Transcription factors and regulatory sites + resources: + - title: .nan + url: .nan - biocontainers: bwa + biotools: bwa bunya: - 0.7.17-gcc-10.3.0 - 0.7.17-gcccore-11.3.0 (D) description: Fast, accurate, memory-efficient aligner for short and long sequencing reads + edam-operations: + - term: Genome indexing + url: http://edamontology.org/operation_3211 + edam-topics: + - term: Mapping + url: http://edamontology.org/topic_0102 galaxy: - description: 'Map with BWA: - map short reads (< 100 bp) against reference genome' title: Map with BWA 0.7.17.5 @@ -1962,17 +2426,26 @@ url: https://doi.org/10.1093/bioinformatics/btu146 - title: Fast and accurate long-read alignment with Burrows-Wheeler transform url: https://doi.org/10.1093/bioinformatics/btp698 - registry-link: bwa - resource-description: .nan - resource-documentation: .nan - topics: - - Mapping + resources: + - title: .nan + url: .nan - biocontainers: bwa-mem2 + biotools: bwa-mem2 bunya: '' description: Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. - galaxy: '' + edam-operations: + - term: Sequence alignment + url: http://edamontology.org/operation_0292 + edam-topics: + - term: Mapping + url: http://edamontology.org/topic_0102 + galaxy: + - description: 'BWA-MEM2: - map medium and long reads (> 100 bp) against reference + genome' + title: BWA-MEM2 2.2.1+galaxy1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbwa_mem2%2Fbwa_mem2%2F2.2.1%2Bgalaxy1 homepage: https://github.com/bwa-mem2/bwa-mem2 id: bwa-mem2 license: MIT @@ -1985,14 +2458,15 @@ publications: - title: Efficient architecture-aware acceleration of BWA-MEM for multicore systems url: https://doi.org/10.1109/IPDPS.2019.00041 - registry-link: bwa-mem2 - resource-description: .nan - resource-documentation: .nan - topics: - - Mapping + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'bwameth: Fast and accurate aligner of BS-Seq reads.' title: bwameth 0.2.6+galaxy0 @@ -2005,13 +2479,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://sourceforge.net/projects/bio-bwa/files/bwakit/ id: bwakit @@ -2020,16 +2496,21 @@ nci-gadi: '' nci-if89: - 0.7.11 + - 0.7.17 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: bx-python + biotools: bx-python bunya: '' description: Tools for manipulating biological data, particularly multiple sequence alignments. + edam-operations: '' + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'Base Coverage: of all intervals' title: Base Coverage 1.0.0 @@ -2079,12 +2560,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: bx-python - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: C3 + biotools: C3 bunya: '' description: Consensus Cancer Driver Gene Caller | Next-generation sequencing has allowed identification of millions of somatic mutations in human cancer cells. @@ -2097,6 +2577,14 @@ users to specify customized operations when calling driver genes, and provides solid statistical evaluations and interpretable visualizations on the integration results + edam-operations: '' + edam-topics: + - term: Genetic variation + url: http://edamontology.org/topic_0199 + - term: Oncology + url: http://edamontology.org/topic_2640 + - term: Sequencing + url: http://edamontology.org/topic_3168 galaxy: - description: 'Copernicus Climate Data Store: for retrieveing climate data' title: Copernicus Climate Data Store 0.1.0 @@ -2111,16 +2599,31 @@ publications: - title: 'C3: Consensus Cancer Driver Gene Caller' url: https://doi.org/10.1016/J.GPB.2018.10.004 - registry-link: C3 - resource-description: .nan - resource-documentation: .nan - topics: - - Genetic variation - - Oncology - - Sequencing + resources: + - title: .nan + url: .nan - biocontainers: cactus + biotools: cactus bunya: '' description: Cactus is a reference-free whole-genome multiple alignment program. + edam-operations: + - term: Multiple sequence alignment + url: http://edamontology.org/operation_0492 + - term: Genome alignment + url: http://edamontology.org/operation_3182 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Phylogeny + url: http://edamontology.org/topic_0084 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Mapping + url: http://edamontology.org/topic_0102 + - term: Phylogenetics + url: http://edamontology.org/topic_3293 galaxy: - description: 'Cactus: whole-genome multiple sequence alignment' title: Cactus 2.7.1+galaxy0 @@ -2145,21 +2648,21 @@ url: https://doi.org/10.1101/gr.123356.111 - title: Cactus graphs for genome comparisons url: https://doi.org/10.1089/cmb.2010.0252 - registry-link: cactus - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Sequence analysis - - Phylogeny - - Sequence assembly - - Mapping - - Phylogenetics + resources: + - title: .nan + url: .nan - biocontainers: camera + biotools: camera bunya: '' description: Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments. + edam-operations: + - term: Sequence annotation + url: http://edamontology.org/operation_0361 + edam-topics: + - term: Metabolomics + url: http://edamontology.org/topic_3172 galaxy: - description: 'CAMERA.annotate: CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.' @@ -2180,17 +2683,22 @@ - title: 'CAMERA: An integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets' url: https://doi.org/10.1021/ac202450g - registry-link: camera - resource-description: .nan - resource-documentation: .nan - topics: - - Metabolomics + resources: + - title: .nan + url: .nan - biocontainers: canu + biotools: canu bunya: - 2.2-gcccore-10.3.0 - 2.2-gcccore-11.3.0 (D) description: De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. + edam-operations: + - term: De-novo assembly + url: http://edamontology.org/operation_0524 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: - description: 'Canu assembler: Assembler optimized for long error-prone reads such as PacBio, Oxford Nanopore' @@ -2212,14 +2720,31 @@ - title: "Canu: Scalable and accurate long-read assembly via adaptive \u03BA-mer\ \ weighting and repeat separation" url: https://doi.org/10.1101/gr.215087.116 - registry-link: canu - resource-description: Testing & optimisation on Gadi (NCI) - resource-documentation: https://github.com/AustralianBioCommons/Canu - topics: - - Genomics + resources: + - title: Testing & optimisation on Gadi (NCI) + url: https://github.com/AustralianBioCommons/Canu - biocontainers: cap3 + biotools: cap3 bunya: '' description: Web-based contig assembly. + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: Mapping assembly + url: http://edamontology.org/operation_0523 + - term: Sequence assembly + url: http://edamontology.org/operation_0310 + - term: Scaffolding + url: http://edamontology.org/operation_3216 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Genetic variation + url: http://edamontology.org/topic_0199 galaxy: - description: 'cap3: Sequence Assembly tool' title: cap3 2.0.0 @@ -2234,19 +2759,27 @@ publications: - title: 'CAP3: A DNA sequence assembly program' url: http://www.ncbi.nlm.nih.gov/pubmed/10508846 - registry-link: cap3 - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - Sequencing - - Sequence analysis - - Genetic variation + resources: + - title: .nan + url: .nan - biocontainers: cardinal + biotools: cardinal bunya: '' description: Implements statistical and computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification. + edam-operations: + - term: Spectral analysis + url: http://edamontology.org/operation_3214 + - term: Standardisation and normalisation + url: http://edamontology.org/operation_3435 + - term: Mass spectra calibration + url: http://edamontology.org/operation_3627 + edam-topics: + - term: Proteomics + url: http://edamontology.org/topic_0121 + - term: Data visualisation + url: http://edamontology.org/topic_0092 galaxy: - description: 'MSI classification: spatial classification of mass spectrometry imaging data' @@ -2287,13 +2820,11 @@ publications: - title: 10.1093/bioinformatics/btv146 url: https://doi.org/10.1093/bioinformatics/btv146 - registry-link: cardinal - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics - - Data visualisation + resources: + - title: .nan + url: .nan - biocontainers: cat_bins + biotools: cat_bins bunya: '' description: Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled @@ -2302,6 +2833,22 @@ gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. + edam-operations: + - term: Taxonomic classification + url: http://edamontology.org/operation_3460 + - term: Sequence assembly + url: http://edamontology.org/operation_0310 + - term: Coding region prediction + url: http://edamontology.org/operation_0436 + edam-topics: + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Metagenomic sequencing + url: http://edamontology.org/topic_3837 + - term: Taxonomy + url: http://edamontology.org/topic_0637 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: - description: 'CAT bins: annotate with taxonomic classification' title: CAT bins 5.0.3.1 @@ -2321,19 +2868,21 @@ - title: Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT url: https://doi.org/10.1186/s13059-019-1817-x - registry-link: cat_bins - resource-description: .nan - resource-documentation: .nan - topics: - - Metagenomics - - Metagenomic sequencing - - Taxonomy - - Sequence assembly + resources: + - title: .nan + url: .nan - biocontainers: cd-hit + biotools: cd-hit bunya: - 4.8.1-gcc-10.3.0 - 4.8.1-gcc-11.3.0 (D) description: Cluster a nucleotide dataset into representative sequences. + edam-operations: + - term: Sequence clustering + url: http://edamontology.org/operation_0291 + edam-topics: + - term: Sequencing + url: http://edamontology.org/topic_3168 galaxy: - description: 'CD-HIT-EST: Cluster a nucleotide dataset into representative sequences' title: CD-HIT-EST 1.3 @@ -2360,16 +2909,25 @@ url: https://doi.org/10.1093/bioinformatics/18.1.77 - title: 10.1093/bioinformatics/btq003 url: https://doi.org/10.1093/bioinformatics/btq003 - registry-link: cd-hit - resource-description: .nan - resource-documentation: .nan - topics: - - Sequencing + resources: + - title: .nan + url: .nan - biocontainers: celseq2 + biotools: celseq2 bunya: - 0.5.3 description: celseq2 is a Python framework for generating the UMI count matrix from CEL-Seq2 sequencing data. + edam-operations: + - term: Demultiplexing + url: http://edamontology.org/operation_3933 + - term: RNA-Seq analysis + url: http://edamontology.org/operation_3680 + edam-topics: + - term: RNA-Seq + url: http://edamontology.org/topic_3170 + - term: Transcriptomics + url: http://edamontology.org/topic_3308 galaxy: '' homepage: https://github.com/yanailab/celseq2 id: celseq2 @@ -2381,16 +2939,28 @@ publications: - title: 'CEL-Seq2: Sensitive highly-multiplexed single-cell RNA-Seq' url: https://doi.org/10.1186/s13059-016-0938-8 - registry-link: celseq2 - resource-description: .nan - resource-documentation: .nan - topics: - - RNA-Seq - - Transcriptomics + resources: + - title: .nan + url: .nan - biocontainers: CellProfiler + biotools: CellProfiler bunya: '' description: Tool for quantifying data from biological images, particularly in high-throughput experiments. + edam-operations: + - term: Quantification + url: http://edamontology.org/operation_3799 + - term: Image analysis + url: http://edamontology.org/operation_3443 + - term: Parsing + url: http://edamontology.org/operation_1812 + edam-topics: + - term: Imaging + url: http://edamontology.org/topic_3382 + - term: Microarray experiment + url: http://edamontology.org/topic_3518 + - term: Genotype and phenotype + url: http://edamontology.org/topic_0625 galaxy: - description: 'TrackObjects: with CellProfiler' title: TrackObjects 3.1.9+galaxy1 @@ -2474,17 +3044,16 @@ url: https://doi.org/10.2144/000112257 - title: 'ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis' url: https://doi.org/10.1002/cpz1.89 - registry-link: CellProfiler - resource-description: .nan - resource-documentation: .nan - topics: - - Imaging - - Microarray experiment - - Genotype and phenotype + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 7.1.0 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger id: cellranger @@ -2495,18 +3064,28 @@ - 6.1.2 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: cellxgene + biotools: cellxgene bunya: '' description: cellxgene (pronounced "cell-by-gene") is an interactive data explorer for single-cell transcriptomics datasets, such as those coming from the Human Cell Atlas. + edam-operations: + - term: Visualisation + url: http://edamontology.org/operation_0337 + - term: Essential dynamics + url: http://edamontology.org/operation_3891 + edam-topics: + - term: Transcriptomics + url: http://edamontology.org/topic_3308 + - term: Cell biology + url: http://edamontology.org/topic_2229 galaxy: - description: 'Interactive CellXgene Environment: ' - title: Interactive CellXgene Environment 0.16.2 + title: Interactive CellXgene Environment 1.1.1 url: https://usegalaxy.org.au/root?tool_id=interactive_tool_cellxgene homepage: https://github.com/chanzuckerberg/cellxgene id: cellxgene @@ -2518,18 +3097,40 @@ publications: - title: 10.1101/2021.04.05.438318 url: https://doi.org/10.1101/2021.04.05.438318 - registry-link: cellxgene - resource-description: .nan - resource-documentation: .nan - topics: - - Transcriptomics - - Cell biology + resources: + - title: .nan + url: .nan - biocontainers: checkm + biotools: checkm bunya: - 1.1.3-foss-2021a - 1.2.2-foss-2022a (D) description: CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. + edam-operations: + - term: Sequence assembly validation + url: http://edamontology.org/operation_3180 + - term: Validation + url: http://edamontology.org/operation_2428 + - term: Sequence composition calculation + url: http://edamontology.org/operation_0236 + - term: Sequencing quality control + url: http://edamontology.org/operation_3218 + - term: Statistical calculation + url: http://edamontology.org/operation_2238 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Phylogenomics + url: http://edamontology.org/topic_0194 + - term: Phylogenetics + url: http://edamontology.org/topic_3293 + - term: Taxonomy + url: http://edamontology.org/topic_0637 + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Data quality management + url: http://edamontology.org/topic_3572 galaxy: '' homepage: https://ecogenomics.github.io/CheckM id: checkm @@ -2542,21 +3143,39 @@ - title: 'CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes' url: https://doi.org/10.1101/gr.186072.114 - registry-link: checkm - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Phylogenomics - - Phylogenetics - - Taxonomy - - Metagenomics - - Data quality management + resources: + - title: .nan + url: .nan - biocontainers: checkm + biotools: checkm bunya: - '2015_01_16' description: CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. + edam-operations: + - term: Sequence assembly validation + url: http://edamontology.org/operation_3180 + - term: Validation + url: http://edamontology.org/operation_2428 + - term: Sequence composition calculation + url: http://edamontology.org/operation_0236 + - term: Sequencing quality control + url: http://edamontology.org/operation_3218 + - term: Statistical calculation + url: http://edamontology.org/operation_2238 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Phylogenomics + url: http://edamontology.org/topic_0194 + - term: Phylogenetics + url: http://edamontology.org/topic_3293 + - term: Taxonomy + url: http://edamontology.org/topic_0637 + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Data quality management + url: http://edamontology.org/topic_3572 galaxy: '' homepage: https://ecogenomics.github.io/CheckM id: checkm-database @@ -2569,21 +3188,25 @@ - title: 'CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes' url: https://doi.org/10.1101/gr.186072.114 - registry-link: checkm - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Phylogenomics - - Phylogenetics - - Taxonomy - - Metagenomics - - Data quality management + resources: + - title: .nan + url: .nan - biocontainers: chembl + biotools: chembl bunya: '' description: Database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. + edam-operations: + - term: Data retrieval + url: http://edamontology.org/operation_2422 + edam-topics: + - term: Small molecules + url: http://edamontology.org/topic_0154 + - term: Chemical biology + url: http://edamontology.org/topic_3369 + - term: Cheminformatics + url: http://edamontology.org/topic_2258 galaxy: - description: 'Search ChEMBL database: for compounds which are similar to a SMILES string' @@ -2607,14 +3230,11 @@ url: https://doi.org/10.1007/s10822-009-9260-9 - title: 'The European Bioinformatics Institute in 2016: Data growth and integration' url: https://doi.org/10.1093/nar/gkv1352 - registry-link: chembl - resource-description: .nan - resource-documentation: .nan - topics: - - Small molecules - - Chemical biology - - Cheminformatics + resources: + - title: .nan + url: .nan - biocontainers: chemfp + biotools: chemfp bunya: '' description: 'Fast cheminformatics fingerprint search, at your fingertips. @@ -2626,6 +3246,22 @@ There are two ways to try out chemfp. From the download page page you can request an evaluation copy of the most recent version of chemfp, or you can download an earlier version for no cost under the MIT license' + edam-operations: + - term: Database search + url: http://edamontology.org/operation_2421 + - term: Standardisation and normalisation + url: http://edamontology.org/operation_3435 + - term: Formatting + url: http://edamontology.org/operation_0335 + edam-topics: + - term: Cheminformatics + url: http://edamontology.org/topic_2258 + - term: Chemistry + url: http://edamontology.org/topic_3314 + - term: Transcription factors and regulatory sites + url: http://edamontology.org/topic_0749 + - term: Literature and language + url: http://edamontology.org/topic_3068 galaxy: - description: 'Molecule to fingerprint: conversion to several different fingerprint formats' @@ -2652,15 +3288,11 @@ url: https://doi.org/10.26434/CHEMRXIV.7877846.V2 - title: The chemfp project url: https://doi.org/10.1186/s13321-019-0398-8 - registry-link: chemfp - resource-description: .nan - resource-documentation: .nan - topics: - - Cheminformatics - - Chemistry - - Transcription factors and regulatory sites - - Literature and language + resources: + - title: .nan + url: .nan - biocontainers: chemicaltoolbox + biotools: chemicaltoolbox bunya: '' description: ChemicalToolbox is a publicly available web server for performing cheminformatics analysis. The ChemicalToolbox provides an intuitive, graphical interface for common @@ -2671,6 +3303,24 @@ we provide four example workflows which illustrate the capabilities of the ChemicalToolbox, covering assembly of a compound library, hole filling, protein-ligand docking, and construction of a quantitative structure-activity relationship (QSAR) model. + edam-operations: + - term: Protein-ligand docking + url: http://edamontology.org/operation_0482 + - term: Molecular dynamics + url: http://edamontology.org/operation_2476 + - term: Sequence assembly + url: http://edamontology.org/operation_0310 + edam-topics: + - term: Cheminformatics + url: http://edamontology.org/topic_2258 + - term: Molecular modelling + url: http://edamontology.org/topic_2275 + - term: Compound libraries and screening + url: http://edamontology.org/topic_3343 + - term: Workflows + url: http://edamontology.org/topic_0769 + - term: Small molecules + url: http://edamontology.org/topic_0154 galaxy: - description: 'Online data: fetching ...' title: Online data 0.2 @@ -2692,22 +3342,33 @@ - title: 'The ChemicalToolbox: Reproducible, user-friendly cheminformatics analysis on the Galaxy platform' url: https://doi.org/10.1186/S13321-020-00442-7 - registry-link: chemicaltoolbox - resource-description: .nan - resource-documentation: .nan - topics: - - Cheminformatics - - Molecular modelling - - Compound libraries and screening - - Workflows - - Small molecules + resources: + - title: .nan + url: .nan - biocontainers: chipseeker + biotools: chipseeker bunya: '' description: This package implements functions to retrieve the nearest genes around the peak, annotate the genomic region of the peak, statistical methods for estimating the significance of overlap among ChIP peak data sets, and incorporate GEO database to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. + edam-operations: + - term: Sequence annotation + url: http://edamontology.org/operation_0361 + - term: Visualisation + url: http://edamontology.org/operation_0337 + - term: Gene-set enrichment analysis + url: http://edamontology.org/operation_2436 + - term: Sequence feature comparison + url: http://edamontology.org/operation_0256 + edam-topics: + - term: ChIP-seq + url: http://edamontology.org/topic_3169 + - term: Data visualisation + url: http://edamontology.org/topic_0092 + - term: Data mining + url: http://edamontology.org/topic_3473 galaxy: - description: 'ChIPseeker: for ChIP peak annotation and visualization' title: ChIPseeker 1.28.3+galaxy0 @@ -2723,17 +3384,22 @@ - title: 'ChIP seeker: An R/Bioconductor package for ChIP peak annotation, comparison and visualization' url: https://doi.org/10.1093/bioinformatics/btv145 - registry-link: chipseeker - resource-description: .nan - resource-documentation: .nan - topics: - - ChIP-seq - - Data visualisation - - Data mining + resources: + - title: .nan + url: .nan - biocontainers: chromeister + biotools: chromeister bunya: '' description: An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons (dotplot). + edam-operations: + - term: Dot plot plotting + url: http://edamontology.org/operation_0490 + edam-topics: + - term: Comparative genomics + url: http://edamontology.org/topic_0797 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'Chromeister: ultra-fast pairwise genome comparisons' title: Chromeister 1.5.a+galaxy1 @@ -2748,15 +3414,15 @@ publications: - title: Ultra-fast genome comparison for large-scale genomic experiments url: https://doi.org/10.1038/s41598-019-46773-w - registry-link: chromeister - resource-description: .nan - resource-documentation: .nan - topics: - - Comparative genomics - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'CIRCexplorer: ' title: CIRCexplorer 1.1.9.0 @@ -2769,14 +3435,16 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 1.5.5--py_3 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://sanger-pathogens.github.io/circlator/ id: circlator @@ -2786,14 +3454,22 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: circos + biotools: circos bunya: '' description: Circos is tool for visualizing data in a circular format. It was developed for genomic data but can work for many other kinds of data as well. + edam-operations: + - term: Visualisation + url: http://edamontology.org/operation_0337 + edam-topics: + - term: Comparative genomics + url: http://edamontology.org/topic_0797 + - term: Data visualisation + url: http://edamontology.org/topic_0092 galaxy: - description: 'Circos: Interval to Circos Text Labels: reformats interval files to prepare for Circos text labels' @@ -2851,15 +3527,15 @@ url: https://doi.org/10.1101/gr.092759.109 - title: 10.7490/f1000research.1114334.1 url: https://doi.org/10.7490/f1000research.1114334.1 - registry-link: circos - resource-description: .nan - resource-documentation: .nan - topics: - - Comparative genomics - - Data visualisation + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'CLIFinder: Find chimerics transcripts containing LINEs sequences' title: CLIFinder 0.5.1 @@ -2872,13 +3548,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'climate stripes: from timeseries' title: climate stripes 1.0.1 @@ -2891,11 +3569,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: clinker + biotools: clinker bunya: '' description: 'Automatic generation of gene cluster comparison figures. @@ -2919,6 +3597,22 @@ clustermap.js is an interactive, reusable d3 chart designed to visualise homology between multiple gene clusters.' + edam-operations: + - term: Sequence clustering + url: http://edamontology.org/operation_0291 + - term: Sequence cluster visualisation + url: http://edamontology.org/operation_0566 + - term: Dendrogram visualisation + url: http://edamontology.org/operation_2938 + edam-topics: + - term: Molecular interactions, pathways and networks + url: http://edamontology.org/topic_0602 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Workflows + url: http://edamontology.org/topic_0769 + - term: Imaging + url: http://edamontology.org/topic_3382 galaxy: - description: 'clinker: Automatic creation of publication-ready gene cluster comparison figures' @@ -2934,17 +3628,15 @@ publications: - title: 10.1101/2020.11.08.370650 url: https://doi.org/10.1101/2020.11.08.370650 - registry-link: clinker - resource-description: .nan - resource-documentation: .nan - topics: - - Molecular interactions, pathways and networks - - Sequence analysis - - Workflows - - Imaging + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'ClipKIT. Alignment trimming software for phylogenetics.: ' title: ClipKIT. Alignment trimming software for phylogenetics. 0.1.0 @@ -2957,14 +3649,20 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: clustalo + biotools: clustalo bunya: '' description: "Multiple sequence alignment software. The name is occassionally spelled\ \ as ClustalOmega, Clustal \u03A9, Clustal\u03A9, Clustal O, ClustalO." + edam-operations: + - term: Multiple sequence alignment + url: http://edamontology.org/operation_0492 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: '' homepage: http://www.clustal.org/omega/ id: clustalo @@ -2982,15 +3680,20 @@ url: https://doi.org/10.1002/pro.3290 - title: 10.1002/0471250953.bi0313s48 url: https://doi.org/10.1002/0471250953.bi0313s48 - registry-link: clustalo - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: clustalw + biotools: clustalw bunya: '' description: Multiple sequence alignment software. Old deprecated versions. Even older versions were CLUSTAL and CLUSTAL V (ClustalV). + edam-operations: + - term: Multiple sequence alignment + url: http://edamontology.org/operation_0492 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'ClustalW: multiple sequence alignment program for DNA or proteins' title: ClustalW 2.1+galaxy1 @@ -3017,15 +3720,32 @@ url: https://doi.org/10.1093/bioinformatics/8.2.189 - title: 'CLUSTAL: a package for performing multiple sequence alignment on a microcomputer' url: https://doi.org/10.1016/0378-1119(88)90330-7 - registry-link: clustalw - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: colabfold + biotools: colabfold bunya: '' description: ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. + edam-operations: + - term: Database search + url: http://edamontology.org/operation_2421 + - term: Protein structure prediction + url: http://edamontology.org/operation_0474 + - term: Fold recognition + url: http://edamontology.org/operation_0303 + edam-topics: + - term: Protein folds and structural domains + url: http://edamontology.org/topic_0736 + - term: Protein folding, stability and design + url: http://edamontology.org/topic_0130 + - term: Structure prediction + url: http://edamontology.org/topic_0082 + - term: Sequence sites, features and motifs + url: http://edamontology.org/topic_0160 + - term: Metagenomics + url: http://edamontology.org/topic_3174 galaxy: '' homepage: http://colabfold.mmseqs.com id: colabfold_batch @@ -3041,18 +3761,15 @@ url: https://doi.org/10.1038/s41592-022-01488-1 - title: 10.1101/2021.08.15.456425 url: https://doi.org/10.1101/2021.08.15.456425 - registry-link: colabfold - resource-description: .nan - resource-documentation: .nan - topics: - - Protein folds and structural domains - - Protein folding, stability and design - - Structure prediction - - Sequence sites, features and motifs - - Metagenomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Combine MetaPhlAn2 and HUMAnN2 outputs: to relate genus/species abundances and gene families/pathways abundances' @@ -3066,13 +3783,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Compose text parameter value: from parameters' title: Compose text parameter value 0.1.1 @@ -3085,13 +3804,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: cookiecutter @@ -3102,13 +3823,15 @@ - 2.4.0 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Count: occurrences of each record' title: Count 1.0.3 @@ -3121,11 +3844,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: cpat + biotools: cpat bunya: '' description: "CPAT (Coding-Potential Assessment Tool) is a logistic regression model-based\ \ classifier that can accurately and quickly distinguish protein-coding and noncoding\ @@ -3133,6 +3856,20 @@ \ takes as input the nucleotides sequences or genomic coordinates of RNAs and\ \ outputs the probabilities p (0 \u2264 p \u2264 1), which measure the likelihood\ \ of protein coding." + edam-operations: + - term: Regression analysis + url: http://edamontology.org/operation_3659 + - term: Query and retrieval + url: http://edamontology.org/operation_0224 + edam-topics: + - term: Functional, regulatory and non-coding RNA + url: http://edamontology.org/topic_0659 + - term: Gene transcripts + url: http://edamontology.org/topic_3512 + - term: RNA-Seq + url: http://edamontology.org/topic_3170 + - term: Transcription factors and regulatory sites + url: http://edamontology.org/topic_0749 galaxy: - description: 'CPAT: coding potential assessment' title: CPAT 3.0.5+galaxy0 @@ -3148,19 +3885,19 @@ - title: RNA Coding Potential Prediction Using Alignment-Free Logistic Regression Model url: https://doi.org/10.1007/978-1-0716-1158-6_3 - registry-link: cpat - resource-description: .nan - resource-documentation: .nan - topics: - - Functional, regulatory and non-coding RNA - - Gene transcripts - - RNA-Seq - - Transcription factors and regulatory sites + resources: + - title: .nan + url: .nan - biocontainers: Crisflash + biotools: Crisflash bunya: - 1.2.0 star-ccm+ description: Software to generate CRISPR guide RNAs against genomes annotated with individual variation. + edam-operations: '' + edam-topics: + - term: Genetic variation + url: http://edamontology.org/topic_0199 galaxy: '' homepage: https://github.com/crisflash/crisflash id: crisflash @@ -3173,14 +3910,15 @@ - title: 'Crisflash: Open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation' url: https://doi.org/10.1093/bioinformatics/btz019 - registry-link: Crisflash - resource-description: .nan - resource-documentation: .nan - topics: - - Genetic variation + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'CTSM/FATES-EMERALD: Functionally Assembled Terrestrial Ecosystem Simulator' @@ -3194,13 +3932,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://developer.nvidia.com/cuda-toolkit id: cuda @@ -3216,16 +3956,20 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: cuDNN + biotools: cuDNN bunya: '' description: "The NVIDIA CUDA\xAE Deep Neural Network library (cuDNN) is a GPU-accelerated\ \ library of primitives for deep neural networks. cuDNN provides highly tuned\ \ implementations for standard routines such as forward and backward convolution,\ \ pooling, normalization, and activation layers." + edam-operations: '' + edam-topics: + - term: Machine learning + url: http://edamontology.org/topic_3474 galaxy: '' homepage: https://developer.nvidia.com/cudnn id: cudnn @@ -3239,17 +3983,28 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: cuDNN - resource-description: .nan - resource-documentation: .nan - topics: - - Machine learning + resources: + - title: .nan + url: .nan - biocontainers: cufflinks + biotools: cufflinks bunya: '' description: Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one. + edam-operations: + - term: RNA-seq time series data analysis + url: http://edamontology.org/operation_3565 + - term: Transcriptome assembly + url: http://edamontology.org/operation_3258 + edam-topics: + - term: RNA splicing + url: http://edamontology.org/topic_3320 + - term: Transcriptomics + url: http://edamontology.org/topic_3308 + - term: RNA-Seq + url: http://edamontology.org/topic_3170 galaxy: - description: 'Cuffcompare: compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments' @@ -3288,18 +4043,23 @@ url: https://doi.org/10.1186/gb-2011-12-3-r22 - title: 10.7490/f1000research.1114334.1 url: https://doi.org/10.7490/f1000research.1114334.1 - registry-link: cufflinks - resource-description: .nan - resource-documentation: .nan - topics: - - RNA splicing - - Transcriptomics - - RNA-Seq + resources: + - title: .nan + url: .nan - biocontainers: cummerbund + biotools: cummerbund bunya: '' description: Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations. + edam-operations: + - term: Sequence analysis + url: http://edamontology.org/operation_2403 + - term: Sequence visualisation + url: http://edamontology.org/operation_0564 + edam-topics: + - term: Sequencing + url: http://edamontology.org/topic_3168 galaxy: - description: 'cummeRbund: visualize Cuffdiff output' title: cummeRbund 2.16.0+galaxy1 @@ -3315,15 +4075,26 @@ - title: 'Erratum: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks (Nature Protocols (2012) 7 (562-578))' url: https://doi.org/10.1038/nprot.2012.016 - registry-link: cummerbund - resource-description: .nan - resource-documentation: .nan - topics: - - Sequencing + resources: + - title: .nan + url: .nan - biocontainers: customprodb + biotools: customprodb bunya: '' description: Generate customized protein sequence database from RNA-Seq data for proteomics search. + edam-operations: + - term: Generation + url: http://edamontology.org/operation_3429 + - term: Sequence annotation + url: http://edamontology.org/operation_0361 + edam-topics: + - term: Data integration and warehousing + url: http://edamontology.org/topic_3366 + - term: RNA-Seq + url: http://edamontology.org/topic_3170 + - term: Sequencing + url: http://edamontology.org/topic_3168 galaxy: - description: 'CustomProDB: Generate protein FASTAs from exosome or transcriptome data' @@ -3340,23 +4111,34 @@ - title: 'CustomProDB: An R package to generate customized protein databases from RNA-Seq data for proteomics search' url: https://doi.org/10.1093/bioinformatics/btt543 - registry-link: customprodb - resource-description: .nan - resource-documentation: .nan - topics: - - Data integration and warehousing - - RNA-Seq - - Sequencing + resources: + - title: .nan + url: .nan - biocontainers: cutadapt + biotools: cutadapt bunya: - 3.4-gcccore-10.3.0 - 4.2-gcccore-11.3.0 (D) description: Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. + edam-operations: + - term: Sequence trimming + url: http://edamontology.org/operation_3192 + - term: Primer removal + url: http://edamontology.org/operation_3237 + - term: Read pre-processing + url: http://edamontology.org/operation_3219 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Probes and primers + url: http://edamontology.org/topic_0632 + - term: Sequencing + url: http://edamontology.org/topic_3168 galaxy: - description: 'Cutadapt: Remove adapter sequences from FASTQ/FASTA' - title: Cutadapt 4.6+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Flparsons%2Fcutadapt%2Fcutadapt%2F4.6%2Bgalaxy1 + title: Cutadapt 4.8+galaxy1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Flparsons%2Fcutadapt%2Fcutadapt%2F4.8%2Bgalaxy1 homepage: https://pypi.org/project/cutadapt/ id: cutadapt license: MIT @@ -3371,14 +4153,11 @@ url: https://doi.org/10.14806/ej.17.1.200 - title: 10.7490/f1000research.1114334.1 url: https://doi.org/10.7490/f1000research.1114334.1 - registry-link: cutadapt - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Probes and primers - - Sequencing + resources: + - title: .nan + url: .nan - biocontainers: cuteSV + biotools: cuteSV bunya: '' description: Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural @@ -3390,6 +4169,20 @@ without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis + edam-operations: + - term: Split read mapping + url: http://edamontology.org/operation_3199 + - term: Genotyping + url: http://edamontology.org/operation_3196 + - term: Structural variation detection + url: http://edamontology.org/operation_3228 + edam-topics: + - term: DNA structural variation + url: http://edamontology.org/topic_3175 + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Computer science + url: http://edamontology.org/topic_3316 galaxy: - description: 'cuteSV: detects long-read-based SVs' title: cuteSV 1.0.8+galaxy0 @@ -3407,14 +4200,11 @@ url: https://doi.org/10.1101/780700 - title: Long-read-based human genomic structural variation detection with cuteSV url: https://doi.org/10.1186/s13059-020-02107-y - registry-link: cuteSV - resource-description: .nan - resource-documentation: .nan - topics: - - DNA structural variation - - Sequencing - - Computer science + resources: + - title: .nan + url: .nan - biocontainers: dada2 + biotools: dada2 bunya: '' description: This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline @@ -3422,40 +4212,54 @@ sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. + edam-operations: + - term: Variant calling + url: http://edamontology.org/operation_3227 + - term: DNA barcoding + url: http://edamontology.org/operation_3200 + edam-topics: + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Genetic variation + url: http://edamontology.org/topic_0199 + - term: Microbial ecology + url: http://edamontology.org/topic_3697 + - term: Metagenomics + url: http://edamontology.org/topic_3174 galaxy: + - description: 'dada2: sequence counts: ' + title: 'dada2: sequence counts 1.30.0+galaxy0' + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_seqcounts%2Fdada2_seqCounts%2F1.30.0%2Bgalaxy0 + - description: 'dada2: removeBimeraDenovo: Remove bimeras from collections of unique + sequences' + title: 'dada2: removeBimeraDenovo 1.30.0+galaxy0' + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_removebimeradenovo%2Fdada2_removeBimeraDenovo%2F1.30.0%2Bgalaxy0 + - description: 'dada2: plotQualityProfile: plot a visual summary of the quality + scores' + title: 'dada2: plotQualityProfile 1.30.0+galaxy0' + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_plotqualityprofile%2Fdada2_plotQualityProfile%2F1.30.0%2Bgalaxy0 + - description: 'dada2: plotComplexity: Plot sequence complexity profile' + title: 'dada2: plotComplexity 1.30.0+galaxy0' + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_plotcomplexity%2Fdada2_plotComplexity%2F1.30.0%2Bgalaxy0 + - description: 'dada2: mergePairs: Merge denoised forward and reverse reads' + title: 'dada2: mergePairs 1.30.0+galaxy0' + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_mergepairs%2Fdada2_mergePairs%2F1.30.0%2Bgalaxy0 + - description: 'dada2: learnErrors: Learn Error rates' + title: 'dada2: learnErrors 1.30.0+galaxy0' + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_learnerrors%2Fdada2_learnErrors%2F1.30.0%2Bgalaxy0 + - description: 'dada2: filterAndTrim: Filter and trim short read data' + title: 'dada2: filterAndTrim 1.30.0+galaxy0' + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_filterandtrim%2Fdada2_filterAndTrim%2F1.30.0%2Bgalaxy0 - description: 'dada2: assignTaxonomy and addSpecies: Learn Error rates' title: 'dada2: assignTaxonomy and addSpecies 1.28+galaxy0' url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_assigntaxonomyaddspecies%2Fdada2_assignTaxonomyAddspecies%2F1.28%2Bgalaxy0 - description: 'dada2: dada: Remove sequencing errors' - title: 'dada2: dada 1.28+galaxy0' - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_dada%2Fdada2_dada%2F1.28%2Bgalaxy0 - - description: 'dada2: filterAndTrim: Filter and trim short read data' - title: 'dada2: filterAndTrim 1.28+galaxy0' - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_filterandtrim%2Fdada2_filterAndTrim%2F1.28%2Bgalaxy0 - - description: 'dada2: learnErrors: Learn Error rates' - title: 'dada2: learnErrors 1.28+galaxy0' - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_learnerrors%2Fdada2_learnErrors%2F1.28%2Bgalaxy0 + title: 'dada2: dada 1.30.0+galaxy0' + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_dada%2Fdada2_dada%2F1.30.0%2Bgalaxy0 - description: 'dada2: makeSequenceTable: construct a sequence table (analogous to OTU table)' - title: 'dada2: makeSequenceTable 1.28+galaxy0' - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_makesequencetable%2Fdada2_makeSequenceTable%2F1.28%2Bgalaxy0 - - description: 'dada2: mergePairs: Merge denoised forward and reverse reads' - title: 'dada2: mergePairs 1.28+galaxy0' - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_mergepairs%2Fdada2_mergePairs%2F1.28%2Bgalaxy0 - - description: 'dada2: plotComplexity: Plot sequence complexity profile' - title: 'dada2: plotComplexity 1.28+galaxy0' - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_plotcomplexity%2Fdada2_plotComplexity%2F1.28%2Bgalaxy0 - - description: 'dada2: plotQualityProfile: plot a visual summary of the quality - scores' - title: 'dada2: plotQualityProfile 1.28+galaxy0' - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_plotqualityprofile%2Fdada2_plotQualityProfile%2F1.28%2Bgalaxy0 - - description: 'dada2: removeBimeraDenovo: Remove bimeras from collections of unique - sequences' - title: 'dada2: removeBimeraDenovo 1.28+galaxy0' - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_removebimeradenovo%2Fdada2_removeBimeraDenovo%2F1.28%2Bgalaxy0 - - description: 'dada2: sequence counts: ' - title: 'dada2: sequence counts 1.28+galaxy0' - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_seqcounts%2Fdada2_seqCounts%2F1.28%2Bgalaxy0 + title: 'dada2: makeSequenceTable 1.30.0+galaxy0' + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdada2_makesequencetable%2Fdada2_makeSequenceTable%2F1.30.0%2Bgalaxy0 homepage: https://bioconductor.org/packages/release/bioc/html/dada2.html id: dada2 license: GPL-3.0 @@ -3466,18 +4270,16 @@ publications: - title: 10.1038/nmeth.3869 url: https://doi.org/10.1038/nmeth.3869 - registry-link: dada2 - resource-description: .nan - resource-documentation: .nan - topics: - - Sequencing - - Genetic variation - - Microbial ecology - - Metagenomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 2.0.5 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://dadi.readthedocs.io/en/latest/ id: dadi @@ -3487,13 +4289,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Datamash: (operations on tabular data)' title: Datamash 1.8+galaxy0 @@ -3506,13 +4310,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Protein Database Downloader: ' title: Protein Database Downloader 0.3.4 @@ -3525,13 +4331,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: dcm2niix @@ -3540,15 +4348,18 @@ nci-gadi: '' nci-if89: - 1.0.20220720 + - 1.0.20230411 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: deepconsensus-cpu @@ -3559,13 +4370,15 @@ - 1.0.0 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: deepconsensus-gpu @@ -3576,16 +4389,26 @@ - 1.2.0 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: deeptools + biotools: deeptools bunya: - 3.5.0-foss-2021a - 3.5.2-foss-2022a (D) description: User-friendly tools for the normalization and visualization of deep-sequencing data. + edam-operations: + - term: Standardisation and normalisation + url: http://edamontology.org/operation_3435 + - term: Visualisation + url: http://edamontology.org/operation_0337 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: ChIP-seq + url: http://edamontology.org/topic_3169 galaxy: - description: 'bamCompare: normalizes and compares two BAM or CRAM files to obtain the ratio, log2ratio or difference between them' @@ -3662,13 +4485,11 @@ publications: - title: 'DeepTools: A flexible platform for exploring deep-sequencing data' url: http://www.ncbi.nlm.nih.gov/pubmed/24799436 - registry-link: deeptools - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - ChIP-seq + resources: + - title: .nan + url: .nan - biocontainers: dendropy + biotools: dendropy bunya: - 4.5.2-gcccore-10.3.0 - 4.5.2-gcccore-11.3.0 (D) @@ -3676,6 +4497,22 @@ classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats. + edam-operations: + - term: Phylogenetic inference + url: http://edamontology.org/operation_0323 + - term: Phylogenetic tree distances calculation + url: http://edamontology.org/operation_0557 + - term: Phylogenetic tree editing + url: http://edamontology.org/operation_0326 + - term: Phylogenetic tree topology analysis + url: http://edamontology.org/operation_0551 + - term: Phylogenetic tree bootstrapping + url: http://edamontology.org/operation_0552 + edam-topics: + - term: Phylogenetics + url: http://edamontology.org/topic_3293 + - term: Phylogenomics + url: http://edamontology.org/topic_0194 galaxy: '' homepage: https://dendropy.org/ id: dendropy @@ -3687,15 +4524,15 @@ publications: - title: 'DendroPy: A Python library for phylogenetic computing' url: https://doi.org/10.1093/bioinformatics/btq228 - registry-link: dendropy - resource-description: .nan - resource-documentation: .nan - topics: - - Phylogenetics - - Phylogenomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Describe samples: and replicates' title: Describe samples 2.15.1+galaxy0 @@ -3708,16 +4545,24 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: deseq2 + biotools: deseq2 bunya: '' description: R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. + edam-operations: + - term: Differential gene expression analysis + url: http://edamontology.org/operation_3223 + - term: RNA-Seq analysis + url: http://edamontology.org/operation_3680 + edam-topics: + - term: RNA-Seq + url: http://edamontology.org/topic_3170 galaxy: - description: 'DESeq2: Determines differentially expressed features from count tables' @@ -3734,12 +4579,11 @@ - title: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 url: https://doi.org/10.1186/s13059-014-0550-8 - registry-link: deseq2 - resource-description: .nan - resource-documentation: .nan - topics: - - RNA-Seq + resources: + - title: .nan + url: .nan - biocontainers: dexseq + biotools: dexseq bunya: '' description: The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions @@ -3747,6 +4591,14 @@ that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. + edam-operations: + - term: Enrichment analysis + url: http://edamontology.org/operation_3501 + - term: Exonic splicing enhancer prediction + url: http://edamontology.org/operation_0446 + edam-topics: + - term: RNA-Seq + url: http://edamontology.org/topic_3170 galaxy: - description: 'plotDEXSeq: Visualization of the per gene DEXSeq results' title: plotDEXSeq 1.48.0+galaxy0 @@ -3768,17 +4620,34 @@ - title: Drift and conservation of differential exon usage across tissues in primate species url: https://doi.org/10.1073/pnas.1307202110 - registry-link: dexseq - resource-description: .nan - resource-documentation: .nan - topics: - - RNA-Seq + resources: + - title: .nan + url: .nan - biocontainers: dfam + biotools: dfam bunya: - 3.3--hdfd78af_0 description: The Dfam database is a open collection of Transposable Element DNA sequence alignments, hidden Markov Models (HMMs), consensus sequences, and genome annotations. + edam-operations: + - term: Genome annotation + url: http://edamontology.org/operation_0362 + - term: Sequence visualisation + url: http://edamontology.org/operation_0564 + - term: Pairwise sequence alignment + url: http://edamontology.org/operation_0491 + edam-topics: + - term: DNA + url: http://edamontology.org/topic_0654 + - term: Phylogeny + url: http://edamontology.org/topic_0084 + - term: Mobile genetic elements + url: http://edamontology.org/topic_0798 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Plant biology + url: http://edamontology.org/topic_0780 galaxy: '' homepage: https://dfam.org id: dfam @@ -3790,16 +4659,11 @@ publications: - title: 10.21203/RS.3.RS-76062/V1 url: https://doi.org/10.21203/RS.3.RS-76062/V1 - registry-link: dfam - resource-description: .nan - resource-documentation: .nan - topics: - - DNA - - Phylogeny - - Mobile genetic elements - - Sequence assembly - - Plant biology + resources: + - title: .nan + url: .nan - biocontainers: DIA-NN + biotools: DIA-NN bunya: '' description: 'Neural networks and interference correction enable deep proteome coverage in high throughput. @@ -3812,6 +4676,24 @@ None required (for .raw, .mzML and .dia processing). Two executables are provided: DiaNN.exe (a command-line tool) and DIA-NN.exe (a GUI implemented as a wrapper for DiaNN.exe)' + edam-operations: + - term: Quantification + url: http://edamontology.org/operation_3799 + - term: Spectral library search + url: http://edamontology.org/operation_3801 + - term: Protein identification + url: http://edamontology.org/operation_3767 + edam-topics: + - term: Proteomics + url: http://edamontology.org/topic_0121 + - term: Proteomics experiment + url: http://edamontology.org/topic_3520 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Machine learning + url: http://edamontology.org/topic_3474 + - term: Small molecules + url: http://edamontology.org/topic_0154 galaxy: - description: 'DIA-NN: is a software for DIA/SWATH data processing' title: DIA-NN 1.8.1+galaxy3 @@ -3827,22 +4709,31 @@ - title: 'DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput' url: https://doi.org/10.1038/S41592-019-0638-X - registry-link: DIA-NN - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics - - Proteomics experiment - - Sequence analysis - - Machine learning - - Small molecules + resources: + - title: .nan + url: .nan - biocontainers: DIA-Umpire + biotools: DIA-Umpire bunya: '' description: DIA-Umpire is an open source Java program for computational analysis of data independent acquisition (DIA) mass spectrometry-based proteomics data. It enables untargeted peptide and protein identification and quantitation using DIA data, and also incorporates targeted extraction to reduce the number of cases of missing quantitation. + edam-operations: + - term: Peak detection + url: http://edamontology.org/operation_3215 + - term: Spectrum calculation + url: http://edamontology.org/operation_3860 + - term: Retention time prediction + url: http://edamontology.org/operation_3633 + - term: Mass spectra calibration + url: http://edamontology.org/operation_3627 + edam-topics: + - term: Proteomics + url: http://edamontology.org/topic_0121 + - term: Proteomics experiment + url: http://edamontology.org/topic_3520 galaxy: - description: 'DIA_Umpire_SE: DIA signal extraction' title: DIA_Umpire_SE 2.1.3.0 @@ -3858,13 +4749,11 @@ - title: 'DIA-Umpire: Comprehensive computational framework for data-independent acquisition proteomics' url: http://www.ncbi.nlm.nih.gov/pubmed/25599550 - registry-link: DIA-Umpire - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics - - Proteomics experiment + resources: + - title: .nan + url: .nan - biocontainers: diamond + biotools: diamond bunya: - 2.0.13-gcc-10.3.0 - 2.1.0-gcc-11.3.0 (D) @@ -3874,6 +4763,14 @@ protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. + edam-operations: + - term: Sequence alignment analysis + url: http://edamontology.org/operation_0258 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Proteins + url: http://edamontology.org/topic_0078 galaxy: - description: 'Diamond: alignment tool for short sequences against a protein database' title: Diamond 2.0.15+galaxy0 @@ -3889,22 +4786,39 @@ license: AGPL-3.0 name: diamond nci-gadi: '' - nci-if89: '' + nci-if89: + - 2.1.9 pawsey: - 2.0.14--hdcc8f71_0 publications: - title: Fast and sensitive protein alignment using DIAMOND url: https://doi.org/10.1038/nmeth.3176 - registry-link: diamond - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis - - Proteins + resources: + - title: .nan + url: .nan - biocontainers: diapasef + biotools: diapasef bunya: '' description: diaPASEF is an appproch for parallel accumulation-serial fragmentation combined with data-independent acquisition. + edam-operations: + - term: Deisotoping + url: http://edamontology.org/operation_3629 + - term: Ion counting + url: http://edamontology.org/operation_3704 + - term: Protein identification + url: http://edamontology.org/operation_3767 + edam-topics: + - term: Proteomics experiment + url: http://edamontology.org/topic_3520 + - term: Proteomics + url: http://edamontology.org/topic_0121 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Small molecules + url: http://edamontology.org/topic_0154 galaxy: - description: 'diapysef library generation: generates spectral library for DIA analysis' @@ -3921,20 +4835,21 @@ - title: "diaPASEF: parallel accumulation\u2013serial fragmentation combined with\ \ data-independent acquisition" url: https://doi.org/10.1038/S41592-020-00998-0 - registry-link: diapasef - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics experiment - - Proteomics - - Sequence analysis - - Sequencing - - Small molecules + resources: + - title: .nan + url: .nan - biocontainers: diffbind + biotools: diffbind bunya: '' description: Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. + edam-operations: + - term: Differential binding analysis + url: http://edamontology.org/operation_3677 + edam-topics: + - term: ChIP-seq + url: http://edamontology.org/topic_3169 galaxy: - description: 'DiffBind: differential binding analysis of ChIP-Seq peak data' title: DiffBind 2.10.0+galaxy1 @@ -3949,14 +4864,15 @@ publications: - title: VAV3 mediates resistance to breast cancer endocrine therapy url: https://doi.org/10.1186/bcr3664 - registry-link: diffbind - resource-description: .nan - resource-documentation: .nan - topics: - - ChIP-seq + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Draw Stacked Bar Plots: for different categories and different criteria' title: Draw Stacked Bar Plots 1.0.0 @@ -3969,13 +4885,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: drishti @@ -3987,16 +4905,28 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: dropletutils + biotools: dropletutils bunya: '' description: Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. + edam-operations: + - term: Loading + url: http://edamontology.org/operation_1812 + edam-topics: + - term: Gene expression + url: http://edamontology.org/topic_0203 + - term: RNA-seq + url: http://edamontology.org/topic_3170 + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Transcriptomics + url: http://edamontology.org/topic_3308 galaxy: - description: 'DropletUtils: Utilities for handling droplet-based single-cell RNA-seq data' @@ -4014,17 +4944,15 @@ url: https://doi.org/10.1101/234872 - title: 10.1101/177048 url: https://doi.org/10.1101/177048 - registry-link: dropletutils - resource-description: .nan - resource-documentation: .nan - topics: - - Gene expression - - RNA-seq - - Sequencing - - Transcriptomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Compute P-values and Correlation Coefficients for Feature Occurrences: between two datasets using Discrete Wavelet Transfoms' @@ -4054,14 +4982,34 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: eagleimp + biotools: eagleimp bunya: - '1.10' description: Fast and Accurate Genome-wide Phasing and Imputation in a Single Tool. + edam-operations: + - term: Imputation + url: http://edamontology.org/operation_3557 + - term: Phasing + url: http://edamontology.org/operation_3454 + - term: Genotyping + url: http://edamontology.org/operation_3196 + - term: Genome indexing + url: http://edamontology.org/operation_3211 + edam-topics: + - term: Genotype and phenotype + url: http://edamontology.org/topic_0625 + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: GWAS study + url: http://edamontology.org/topic_3517 + - term: DNA + url: http://edamontology.org/topic_0654 + - term: Computer science + url: http://edamontology.org/topic_3316 galaxy: '' homepage: https://github.com/ikmb/eagleimp id: eagleimp @@ -4073,21 +5021,22 @@ publications: - title: 10.1101/2022.01.11.475810 url: https://doi.org/10.1101/2022.01.11.475810 - registry-link: eagleimp - resource-description: .nan - resource-documentation: .nan - topics: - - Genotype and phenotype - - Sequencing - - GWAS study - - DNA - - Computer science + resources: + - title: .nan + url: .nan - biocontainers: easybuild + biotools: easybuild bunya: - 4.8.0 description: EasyBuild is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way. + edam-operations: + - term: Service management + url: http://edamontology.org/operation_3760 + edam-topics: + - term: Computer science + url: http://edamontology.org/topic_3316 galaxy: '' homepage: https://github.com/easybuilders/easybuild id: easybuild @@ -4097,14 +5046,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: easybuild - resource-description: .nan - resource-documentation: .nan - topics: - - Computer science + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'EBI SRA: ENA SRA' title: EBI SRA 1.0.1 @@ -4117,11 +5067,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: edger + biotools: edger bunya: '' description: Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on @@ -4129,6 +5079,16 @@ tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. + edam-operations: + - term: Differential gene expression analysis + url: http://edamontology.org/operation_3223 + edam-topics: + - term: Genetics + url: http://edamontology.org/topic_3053 + - term: RNA-Seq + url: http://edamontology.org/topic_3170 + - term: ChIP-seq + url: http://edamontology.org/topic_3169 galaxy: - description: 'edgeR: Perform differential expression of count data' title: edgeR 3.36.0+galaxy4 @@ -4150,14 +5110,11 @@ - title: 'From reads to genes to pathways: Differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline' url: https://doi.org/10.12688/f1000research.8987.2 - registry-link: edger - resource-description: .nan - resource-documentation: .nan - topics: - - Genetics - - RNA-Seq - - ChIP-seq + resources: + - title: .nan + url: .nan - biocontainers: edger + biotools: edger bunya: '' description: Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on @@ -4165,6 +5122,16 @@ tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. + edam-operations: + - term: Differential gene expression analysis + url: http://edamontology.org/operation_3223 + edam-topics: + - term: Genetics + url: http://edamontology.org/topic_3053 + - term: RNA-Seq + url: http://edamontology.org/topic_3170 + - term: ChIP-seq + url: http://edamontology.org/topic_3169 galaxy: - description: 'edgeR-repenrich: Determines differentially expressed features from RepEnrich counts' @@ -4187,20 +5154,23 @@ - title: 'From reads to genes to pathways: Differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline' url: https://doi.org/10.12688/f1000research.8987.2 - registry-link: edger - resource-description: .nan - resource-documentation: .nan - topics: - - Genetics - - RNA-Seq - - ChIP-seq + resources: + - title: .nan + url: .nan - biocontainers: edirect + biotools: edirect bunya: - '16.2' description: Entrez Direct (EDirect) is a command-line tool for Entrez databases. EDirect connects to Entrez through the Entrez Programming Utilities interface. It supports searching by indexed terms, looking up precomputed neighbors or links, filtering results by date or category, and downloading record summaries or reports. + edam-operations: + - term: Information retrieval + url: http://edamontology.org/operation_3908 + edam-topics: + - term: Data integration and warehousing + url: http://edamontology.org/topic_3366 galaxy: '' homepage: https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect id: edirect @@ -4210,12 +5180,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: edirect - resource-description: .nan - resource-documentation: .nan - topics: - - Data integration and warehousing + resources: + - title: .nan + url: .nan - biocontainers: eggnog-mapper + biotools: eggnog-mapper bunya: '' description: 'For fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database to transfer functional @@ -4226,6 +5195,14 @@ The use of orthology predictions for functional annotation permits a higher precision than traditional homology searches, as it avoids transferring annotations from close paralogs.' + edam-operations: + - term: Database search + url: http://edamontology.org/operation_2421 + edam-topics: + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: - description: 'eggNOG Mapper: functional sequence annotation by orthology' title: eggNOG Mapper 2.1.8+galaxy4 @@ -4253,16 +5230,20 @@ - title: 'eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale' url: https://doi.org/10.1093/molbev/msab293 - registry-link: eggnog-mapper - resource-description: .nan - resource-documentation: .nan - topics: - - Metagenomics - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: egsea + biotools: egsea bunya: '' description: This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. + edam-operations: + - term: Gene set testing + url: http://edamontology.org/operation_3224 + edam-topics: + - term: Systems biology + url: http://edamontology.org/topic_2259 galaxy: - description: 'EGSEA: easy and efficient ensemble gene set testing' title: EGSEA 1.20.0 @@ -4278,12 +5259,11 @@ - title: Combining multiple tools outperforms individual methods in gene set enrichment analyses url: https://doi.org/10.1093/bioinformatics/btw623 - registry-link: egsea - resource-description: .nan - resource-documentation: .nan - topics: - - Systems biology + resources: + - title: .nan + url: .nan - biocontainers: elastix + biotools: elastix bunya: '' description: 'Evaluation of an Open Source Registration Package for Automatic Contour Propagation in Online Adaptive Intensity-Modulated Proton Therapy of Prostate @@ -4304,6 +5284,16 @@ automated processing of large numbers of data sets, by means of scripting. Nowadays elastix is accompanied by SimpleElastix , making it available in languages like C++, Python, Java, R, Ruby, C# and Lua.' + edam-operations: + - term: Image analysis + url: http://edamontology.org/operation_3443 + edam-topics: + - term: Medical imaging + url: http://edamontology.org/topic_3384 + - term: Oncology + url: http://edamontology.org/topic_2640 + - term: Model organisms + url: http://edamontology.org/topic_0621 galaxy: '' homepage: http://elastix.isi.uu.nl id: elastix @@ -4312,6 +5302,7 @@ nci-gadi: '' nci-if89: - 4.9.0 + - 5.1.0 pawsey: '' publications: - title: 'Elastix: A toolbox for intensity-based medical image registration' @@ -4323,17 +5314,32 @@ Propagation in Online Adaptive Intensity-Modulated Proton Therapy of Prostate Cancer url: https://doi.org/10.3389/FONC.2019.01297 - registry-link: elastix - resource-description: .nan - resource-documentation: .nan - topics: - - Medical imaging - - Oncology - - Model organisms + resources: + - title: .nan + url: .nan - biocontainers: emboss + biotools: emboss bunya: '' description: Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. + edam-operations: + - term: Sequence analysis + url: http://edamontology.org/operation_2403 + - term: Local alignment + url: http://edamontology.org/operation_0495 + - term: Sequence alignment analysis + url: http://edamontology.org/operation_0258 + - term: Global alignment + url: http://edamontology.org/operation_0496 + - term: Sequence alignment + url: http://edamontology.org/operation_0292 + edam-topics: + - term: Molecular biology + url: http://edamontology.org/topic_3047 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Biology + url: http://edamontology.org/topic_3070 galaxy: - description: 'dreg: Regular expression search of a nucleotide sequence' title: dreg 5.0.0+galaxy1 @@ -4668,20 +5674,35 @@ publications: - title: 'EMBOSS: The European Molecular Biology Open Software Suite' url: http://www.ncbi.nlm.nih.gov/pubmed/10827456 - registry-link: emboss - resource-description: .nan - resource-documentation: .nan - topics: - - Molecular biology - - Sequence analysis - - Biology + resources: + - title: .nan + url: .nan - biocontainers: ena + biotools: ena bunya: '' description: A globally comprehensive data resource for nucleotide sequence, spanning raw data, alignments and assemblies, functional and taxonomic annotation and rich contextual data relating to sequenced samples and experimental design. Serving both as the database of record for the output of the world's sequencing activity and as a platform for the management, sharing and publication of sequence data. + edam-operations: + - term: Sequence similarity search + url: http://edamontology.org/operation_0346 + - term: Deposition + url: http://edamontology.org/operation_3431 + - term: Sequence assembly + url: http://edamontology.org/operation_0310 + - term: Data retrieval + url: http://edamontology.org/operation_2422 + edam-topics: + - term: Data submission, annotation and curation + url: http://edamontology.org/topic_0219 + - term: Transcription factors and regulatory sites + url: http://edamontology.org/topic_0749 + - term: Gene transcripts + url: http://edamontology.org/topic_3512 + - term: Nucleic acid sites, features and motifs + url: http://edamontology.org/topic_3511 galaxy: - description: 'ENA Upload tool: Submission of (meta)data to the European Nucleotide Archive (ENA)' @@ -4703,19 +5724,23 @@ url: http://www.ncbi.nlm.nih.gov/pubmed/27899630 - title: 10.1093/BIOINFORMATICS/BTAB421 url: https://doi.org/10.1093/BIOINFORMATICS/BTAB421 - registry-link: ena - resource-description: .nan - resource-documentation: .nan - topics: - - Data submission, annotation and curation - - Transcription factors and regulatory sites - - Gene transcripts - - Nucleic acid sites, features and motifs + resources: + - title: .nan + url: .nan - biocontainers: EncyclopeDIA + biotools: EncyclopeDIA bunya: '' description: EncyclopeDIA is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries. + edam-operations: + - term: Formatting + url: http://edamontology.org/operation_0335 + edam-topics: + - term: Proteomics + url: http://edamontology.org/topic_0121 + - term: Proteomics experiment + url: http://edamontology.org/topic_3520 galaxy: - description: 'SearchToLib: Build a Chromatogram Library from Data-Independent Acquisition (DIA) MS/MS Data' @@ -4744,16 +5769,16 @@ - title: Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry url: http://www.ncbi.nlm.nih.gov/pubmed/30510204 - registry-link: EncyclopeDIA - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics - - Proteomics experiment + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 0.6.5 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://github.com/geronimp/enrichM id: enrichm @@ -4763,13 +5788,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: ensembl-vep @@ -4780,13 +5807,15 @@ - '106.1' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: ete3 @@ -4797,13 +5826,15 @@ - 3.1.3 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'EtherCalc: ' title: EtherCalc 0.1 @@ -4816,16 +5847,36 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: eupathdb + biotools: eupathdb bunya: '' description: Integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. The database portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + edam-operations: + - term: Database search + url: http://edamontology.org/operation_2421 + - term: Deposition + url: http://edamontology.org/operation_3431 + - term: Generation + url: http://edamontology.org/operation_3429 + - term: Query and retrieval + url: http://edamontology.org/operation_0224 + - term: Data retrieval + url: http://edamontology.org/operation_2422 + edam-topics: + - term: Model organisms + url: http://edamontology.org/topic_0621 + - term: Model organisms + url: http://edamontology.org/topic_0621 + - term: Zoology + url: http://edamontology.org/topic_3500 + - term: Gene transcripts + url: http://edamontology.org/topic_3512 galaxy: - description: 'EuPathDB: server' title: EuPathDB 1.0.0 @@ -4840,18 +5891,24 @@ publications: - title: 'EuPathDB: A portal to eukaryotic pathogen databases' url: http://www.ncbi.nlm.nih.gov/pubmed/19914931 - registry-link: eupathdb - resource-description: .nan - resource-documentation: .nan - topics: - - Model organisms - - Model organisms - - Zoology - - Gene transcripts + resources: + - title: .nan + url: .nan - biocontainers: exabayes + biotools: exabayes bunya: '' description: ExaBayes is a software package for Bayesian phylogenetic tree inference. It is particularly suitable for large-scale analyses on computer clusters. + edam-operations: + - term: Phylogenetic inference + url: http://edamontology.org/operation_0323 + - term: Phylogenetic tree editing + url: http://edamontology.org/operation_0326 + - term: Phylogenetic tree topology analysis + url: http://edamontology.org/operation_0551 + edam-topics: + - term: Phylogenetics + url: http://edamontology.org/topic_3293 galaxy: '' homepage: https://github.com/aberer/exabayes id: exabayes @@ -4862,14 +5919,23 @@ pawsey: - 1.5.1 publications: '' - registry-link: exabayes - resource-description: .nan - resource-documentation: .nan - topics: - - Phylogenetics + resources: + - title: .nan + url: .nan - biocontainers: ExaML + biotools: ExaML bunya: '' description: Tool for phylogenomic analyses on supercomputers. + edam-operations: + - term: Phylogenetic tree generation (maximum likelihood and Bayesian methods) + url: http://edamontology.org/operation_0547 + edam-topics: + - term: Phylogeny + url: http://edamontology.org/topic_0084 + - term: Phylogenomics + url: http://edamontology.org/topic_0194 + - term: Literature and language + url: http://edamontology.org/topic_3068 galaxy: '' homepage: https://github.com/stamatak/ExaML id: examl @@ -4882,18 +5948,29 @@ publications: - title: 'ExaML version 3: A tool for phylogenomic analyses on supercomputers' url: https://doi.org/10.1093/bioinformatics/btv184 - registry-link: ExaML - resource-description: .nan - resource-documentation: .nan - topics: - - Phylogeny - - Phylogenomics - - Literature and language + resources: + - title: .nan + url: .nan - biocontainers: exonerate + biotools: exonerate bunya: - 2.4.0--hf34a1b8_7 description: A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. + edam-operations: + - term: Pairwise sequence alignment + url: http://edamontology.org/operation_0491 + - term: Protein threading + url: http://edamontology.org/operation_0302 + - term: Genome alignment + url: http://edamontology.org/operation_3182 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Sequence sites, features and motifs + url: http://edamontology.org/topic_0160 + - term: Molecular interactions, pathways and networks + url: http://edamontology.org/topic_0602 galaxy: - description: 'Exonerate: pairwise sequence comparison' title: Exonerate 2.4.0+galaxy2 @@ -4910,16 +5987,15 @@ publications: - title: Automated generation of heuristics for biological sequence comparison url: http://www.ncbi.nlm.nih.gov/pubmed/15713233 - registry-link: exonerate - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis - - Sequence sites, features and motifs - - Molecular interactions, pathways and networks + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Export datasets: to remote files source' title: Export datasets 0.1.0 @@ -4932,15 +6008,25 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: export2graphlan + biotools: export2graphlan bunya: '' description: export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. + edam-operations: + - term: Conversion + url: http://edamontology.org/operation_3434 + edam-topics: + - term: Taxonomy + url: http://edamontology.org/topic_0637 + - term: Metabolomics + url: http://edamontology.org/topic_3172 + - term: Biomarkers + url: http://edamontology.org/topic_3360 galaxy: - description: 'Export to GraPhlAn: ' title: Export to GraPhlAn 0.20+galaxy0 @@ -4956,14 +6042,11 @@ - title: Compact graphical representation of phylogenetic data and metadata with GraPhlAn url: https://doi.org/10.7717/peerj.1029 - registry-link: export2graphlan - resource-description: .nan - resource-documentation: .nan - topics: - - Taxonomy - - Metabolomics - - Biomarkers + resources: + - title: .nan + url: .nan - biocontainers: express + biotools: express bunya: '' description: Streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq @@ -4971,6 +6054,18 @@ transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data. It can be used to resolve ambiguous mappings in other high-throughput sequencing based applications. + edam-operations: + - term: Imputation + url: http://edamontology.org/operation_3557 + edam-topics: + - term: Gene expression + url: http://edamontology.org/topic_0203 + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: RNA-seq + url: http://edamontology.org/topic_3170 + - term: ChIP-seq + url: http://edamontology.org/topic_3169 galaxy: - description: 'eXpress: Quantify the abundances of a set of target sequences from sampled subsequences' @@ -4988,18 +6083,16 @@ url: https://doi.org/10.1186/gb-2011-12-3-r22 - title: 10.7490/f1000research.1114334.1 url: https://doi.org/10.7490/f1000research.1114334.1 - registry-link: express - resource-description: .nan - resource-documentation: .nan - topics: - - Gene expression - - Metagenomics - - RNA-seq - - ChIP-seq + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 1.1--h0326b38_1 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: f5c @@ -5010,14 +6103,20 @@ - '1.3' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: falcon + biotools: falcon bunya: - 0.0.8--hdfd78af_1 description: Experimental PacBio diploid assembler. + edam-operations: + - term: Sequence assembly + url: http://edamontology.org/operation_0310 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: '' homepage: https://github.com/pratas/falcon id: pb-assembly @@ -5029,14 +6128,23 @@ publications: - title: 10.5281/zenodo.35745 url: https://doi.org/10.5281/zenodo.35745 - registry-link: falcon - resource-description: Install, optimisation and testing at Pawsey - resource-documentation: https://github.com/AustralianBioCommons/falcon - topics: - - Sequence assembly + resources: + - title: Install, optimisation and testing at Pawsey + url: https://github.com/AustralianBioCommons/falcon - biocontainers: compute_sequence_length + biotools: compute_sequence_length bunya: '' description: Add length of sequence to fasta header. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + edam-topics: + - term: Nucleic acids + url: http://edamontology.org/topic_0077 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Data management + url: http://edamontology.org/topic_3071 galaxy: - description: 'Compute sequence length: ' title: Compute sequence length 1.0.3 @@ -5054,16 +6162,15 @@ url: https://doi.org/10.1093/nar/gkw343 - title: 10.7490/f1000research.1114334.1 url: https://doi.org/10.7490/f1000research.1114334.1 - registry-link: compute_sequence_length - resource-description: .nan - resource-documentation: .nan - topics: - - Nucleic acids - - Sequence analysis - - Data management + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Concatenate: FASTA alignment by species' title: Concatenate 0.0.1 @@ -5076,13 +6183,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Filter sequences by length: ' title: Filter sequences by length 1.2 @@ -5095,13 +6204,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'FASTA Merge Files and Filter Unique Sequences: Concatenate FASTA database files together' @@ -5115,13 +6226,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Fasta Statistics: display summary statistics for a FASTA file' title: Fasta Statistics 2.0 @@ -5134,13 +6247,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'FASTA-to-Tabular: converter' title: FASTA-to-Tabular 1.1.1 @@ -5153,14 +6268,16 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 1.0.0-gcccore-10.3.0 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: fastahack @@ -5170,17 +6287,27 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: fastani + biotools: fastani bunya: - 1.33-gcc-10.3.0 description: FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. + edam-operations: + - term: Genome alignment + url: http://edamontology.org/operation_3182 + - term: Sequence similarity search + url: http://edamontology.org/operation_0346 + edam-topics: + - term: Microbiology + url: http://edamontology.org/topic_3301 + - term: Genetic variation + url: http://edamontology.org/topic_0199 galaxy: '' homepage: https://github.com/ParBLiSS/FastANI id: fastani @@ -5190,17 +6317,21 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: fastani - resource-description: .nan - resource-documentation: .nan - topics: - - Microbiology - - Genetic variation + resources: + - title: .nan + url: .nan - biocontainers: fastool + biotools: fastool bunya: - 0.1.4--h7132678_6 description: Read huge FastQ and FastA files (both normal and gzipped) an demanipulate them. + edam-operations: + - term: Formatting + url: http://edamontology.org/operation_0335 + edam-topics: + - term: Data management + url: http://edamontology.org/topic_3071 galaxy: '' homepage: https://github.com/fstrozzi/Fastool id: fastool @@ -5210,17 +6341,26 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: fastool - resource-description: .nan - resource-documentation: .nan - topics: - - Data management + resources: + - title: .nan + url: .nan - biocontainers: fastp + biotools: fastp bunya: - 0.23.2-gcc-11.3.0 description: A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. + edam-operations: + - term: Sequencing quality control + url: http://edamontology.org/operation_3218 + - term: Sequence contamination filtering + url: http://edamontology.org/operation_3187 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Probes and primers + url: http://edamontology.org/topic_0632 galaxy: - description: 'fastp: fast all-in-one preprocessing for FASTQ files' title: fastp 0.23.4+galaxy0 @@ -5236,13 +6376,11 @@ publications: - title: 10.1093/bioinformatics/bty560 url: https://doi.org/10.1093/bioinformatics/bty560 - registry-link: fastp - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis - - Probes and primers + resources: + - title: .nan + url: .nan - biocontainers: fastqc + biotools: fastqc bunya: - 0.11.9-java-11 description: This tool aims to provide a QC report which can spot problems or biases @@ -5252,6 +6390,20 @@ can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. + edam-operations: + - term: Sequence composition calculation + url: http://edamontology.org/operation_0236 + - term: Sequencing quality control + url: http://edamontology.org/operation_3218 + - term: Statistical calculation + url: http://edamontology.org/operation_2238 + edam-topics: + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Data quality management + url: http://edamontology.org/topic_3572 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'FastQC: Read Quality reports' title: FastQC 0.74+galaxy0 @@ -5269,16 +6421,15 @@ publications: - title: 10.7490/f1000research.1114334.1 url: https://doi.org/10.7490/f1000research.1114334.1 - registry-link: fastqc - resource-description: .nan - resource-documentation: .nan - topics: - - Sequencing - - Data quality management - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: "FASTQE: visualize fastq files with emoji's \U0001F9EC\U0001F60E" title: FASTQE 0.2.6+galaxy2 @@ -5291,15 +6442,25 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: fasttree + biotools: fasttree bunya: - 2.1.11-gcccore-10.3.0 description: Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. + edam-operations: + - term: Phylogenetic tree generation (from molecular sequences) + url: http://edamontology.org/operation_0540 + - term: Phylogenetic tree generation (maximum likelihood and Bayesian methods) + url: http://edamontology.org/operation_0547 + edam-topics: + - term: Phylogenetics + url: http://edamontology.org/topic_3293 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'FASTTREE: build maximum-likelihood phylogenetic trees' title: FASTTREE 2.1.10+galaxy1 @@ -5317,16 +6478,22 @@ url: https://doi.org/10.1093/molbev/msp077 - title: 10.1371/journal.pone.0009490 url: https://doi.org/10.1371/journal.pone.0009490 - registry-link: fasttree - resource-description: .nan - resource-documentation: .nan - topics: - - Phylogenetics - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: fastx-toolkit + biotools: fastx-toolkit bunya: '' description: Collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. + edam-operations: + - term: Read pre-processing + url: http://edamontology.org/operation_3219 + - term: Sequence editing + url: http://edamontology.org/operation_0231 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'Remove sequencing artifacts: ' title: Remove sequencing artifacts 1.0.1+galaxy2 @@ -5365,15 +6532,22 @@ publications: - title: Comparison of DNA sequences with protein sequences url: https://doi.org/10.1006/geno.1997.4995 - registry-link: fastx-toolkit - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: fastx-toolkit + biotools: fastx-toolkit bunya: '' description: Collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. + edam-operations: + - term: Read pre-processing + url: http://edamontology.org/operation_3219 + - term: Sequence editing + url: http://edamontology.org/operation_0231 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'Length Distribution: chart' title: Length Distribution 1.0.1+galaxy2 @@ -5400,15 +6574,16 @@ publications: - title: Comparison of DNA sequences with protein sequences url: https://doi.org/10.1006/geno.1997.4995 - registry-link: fastx-toolkit - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 20190320-gcccore-10.3.0 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: fermi-lite @@ -5418,14 +6593,20 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: fgenesh + biotools: fgenesh bunya: '' description: HMM-based gene structure prediction (multiple genes, both chains); Program for predicting multiple genes in genomic DNA sequences. + edam-operations: + - term: Gene prediction + url: http://edamontology.org/operation_2454 + edam-topics: + - term: Gene structure + url: http://edamontology.org/topic_0114 galaxy: - description: 'FGENESH get protein: sequences using rensn3 files' title: FGENESH get protein 1.0.0+galaxy0 @@ -5440,17 +6621,22 @@ publications: - title: 10.1186/gb-2006-7-s1-s10 url: https://doi.org/10.1186/gb-2006-7-s1-s10 - registry-link: fgenesh - resource-description: Fgenesh++ - resource-documentation: https://support.pawsey.org.au/documentation/pages/viewpage.action?pageId=68818716 - topics: - - Gene structure + resources: + - title: Fgenesh++ + url: https://support.pawsey.org.au/documentation/pages/viewpage.action?pageId=68818716 - biocontainers: fgsea + biotools: fgsea bunya: '' description: The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. + edam-operations: + - term: Gene-set enrichment analysis + url: http://edamontology.org/operation_2436 + edam-topics: + - term: Genetics + url: http://edamontology.org/topic_3053 galaxy: - description: 'fgsea: - fast preranked gene set enrichment analysis' title: fgsea 1.8.0+galaxy1 @@ -5465,14 +6651,15 @@ publications: - title: 10.1101/060012 url: https://doi.org/10.1101/060012 - registry-link: fgsea - resource-description: .nan - resource-documentation: .nan - topics: - - Genetics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Filter Combined Transcripts: using tracking file' title: Filter Combined Transcripts 0.1 @@ -5485,16 +6672,22 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: filtlong + biotools: filtlong bunya: '' description: Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. + edam-operations: + - term: Filtering + url: http://edamontology.org/operation_3695 + - term: Sequencing quality control + url: http://edamontology.org/operation_3218 + edam-topics: '' galaxy: - description: 'filtlong: Filtering long reads by quality' title: filtlong 0.2.1+galaxy0 @@ -5507,14 +6700,22 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: filtlong - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: flashlfq + biotools: flashlfq bunya: '' description: FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. + edam-operations: + - term: Label-free quantification + url: http://edamontology.org/operation_3634 + edam-topics: + - term: Proteomics experiment + url: http://edamontology.org/topic_3520 + - term: Proteomics + url: http://edamontology.org/topic_0121 galaxy: - description: 'FlashLFQ: ultrafast label-free quantification for mass-spectrometry proteomics' @@ -5528,18 +6729,18 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: flashlfq - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics experiment - - Proteomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 2.6.4-gcccore-10.3.0 - 2.6.4-gcccore-11.3.0 - 2.6.4-gcccore-12.3.0 (D) description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: flex @@ -5549,11 +6750,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: Flye + biotools: Flye bunya: - 2.9-gcc-10.3.0 description: 'Flye is a de novo assembler for single molecule sequencing reads, @@ -5561,6 +6762,24 @@ for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.' + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: De-novo assembly + url: http://edamontology.org/operation_0524 + - term: Mapping assembly + url: http://edamontology.org/operation_0523 + - term: Cross-assembly + url: http://edamontology.org/operation_3730 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Whole genome sequencing + url: http://edamontology.org/topic_3673 + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: - description: 'Flye: de novo assembler for single molecule sequencing reads' title: Flye 2.9.3+galaxy0 @@ -5573,6 +6792,7 @@ nci-if89: - '2.9' - 2.9.1 + - 2.9.3 pawsey: '' publications: - title: Comparison of long-read sequencing technologies in the hybrid assembly @@ -5582,17 +6802,15 @@ url: https://doi.org/10.1038/s41587-019-0072-8 - title: 'metaFlye: scalable long-read metagenome assembly using repeat graphs' url: https://doi.org/10.1038/s41592-020-00971-x - registry-link: Flye - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - Metagenomics - - Whole genome sequencing - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Flymine: server' title: Flymine 1.0.0 @@ -5605,15 +6823,21 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: foldseek + biotools: foldseek bunya: '' description: Foldseek enables fast and sensitive comparisons of large structure sets. It reaches sensitivities similar to state-of-the-art structural aligners while being at least 20,000 times faster. + edam-operations: + - term: Structure alignment + url: http://edamontology.org/operation_0295 + edam-topics: + - term: Proteins + url: http://edamontology.org/topic_0078 galaxy: '' homepage: https://foldseek.com id: foldseek @@ -5628,17 +6852,22 @@ url: https://doi.org/10.1038/s41587-023-01773-0 - title: 10.1101/2022.02.07.479398 url: https://doi.org/10.1101/2022.02.07.479398 - registry-link: foldseek - resource-description: .nan - resource-documentation: .nan - topics: - - Proteins + resources: + - title: .nan + url: .nan - biocontainers: fpocket + biotools: fpocket bunya: '' description: Web server which detects small molecule pockets by relying on the geometric alpha sphere theory. It also tracks pockets during molecular dynamics so to provide insight on pocket dynamics (mdpocket) and transposes mdpocket to the combined analysis of homologous structures (hpocket). + edam-operations: + - term: Molecular surface analysis + url: http://edamontology.org/operation_3351 + edam-topics: + - term: Protein structural motifs and surfaces + url: http://edamontology.org/topic_0166 galaxy: - description: 'dpocket: to calculate descriptors for protein pockets' title: dpocket 4.0.0+galaxy0 @@ -5658,14 +6887,21 @@ url: http://www.ncbi.nlm.nih.gov/pubmed/20478829 - title: 'Fpocket: An open source platform for ligand pocket detection' url: http://www.ncbi.nlm.nih.gov/pubmed/19486540 - registry-link: fpocket - resource-description: .nan - resource-documentation: .nan - topics: - - Protein structural motifs and surfaces + resources: + - title: .nan + url: .nan - biocontainers: fraggenescan + biotools: fraggenescan bunya: '' description: Application for finding (fragmented) genes in short reads + edam-operations: + - term: Gene prediction + url: http://edamontology.org/operation_2454 + edam-topics: + - term: Genetics + url: http://edamontology.org/topic_3053 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'FragGeneScan: for finding (fragmented) genes in short reads' title: FragGeneScan 1.30.0 @@ -5682,19 +6918,29 @@ url: http://www.ncbi.nlm.nih.gov/pubmed/20805240 - title: 10.7490/f1000research.1114334.1 url: https://doi.org/10.7490/f1000research.1114334.1 - registry-link: fraggenescan - resource-description: .nan - resource-documentation: .nan - topics: - - Genetics - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: freebayes + biotools: freebayes bunya: - 1.3.6-foss-2021a-r-4.1.0 description: Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. + edam-operations: + - term: Variant calling + url: http://edamontology.org/operation_3227 + - term: Statistical calculation + url: http://edamontology.org/operation_2238 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Genetic variation + url: http://edamontology.org/topic_0199 + - term: Rare diseases + url: http://edamontology.org/topic_3325 galaxy: - description: 'BamLeftAlign: indels in BAM datasets' title: BamLeftAlign 1.3.6 @@ -5710,17 +6956,16 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: freebayes - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Genetic variation - - Rare diseases + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 20141119-gcccore-10.3.0 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: fsom @@ -5730,14 +6975,20 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: funannotate + biotools: funannotate bunya: '' description: funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). + edam-operations: + - term: Genome annotation + url: http://edamontology.org/operation_0362 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: - description: 'Funannotate functional: annotation' title: Funannotate functional 1.8.15+galaxy5 @@ -5762,14 +7013,21 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: funannotate - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: gaeval + biotools: gaeval bunya: '' description: Gene Annotation EVAluation. + edam-operations: + - term: Sequence annotation + url: http://edamontology.org/operation_0361 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Gene structure + url: http://edamontology.org/topic_0114 galaxy: - description: 'AEGeAn CanonGFF3: pre-process GFF3 files, removing all features not directly related to protein-coding genes' @@ -5795,15 +7053,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: gaeval - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis - - Gene structure + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Bundle Collection: Package up and download a collection of files as a single archive.' @@ -5862,13 +7120,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'AXT to concatenated FASTA: Converts an AXT formatted file to a concatenated FASTA alignment' @@ -5880,6 +7140,190 @@ - description: 'AXT to LAV: Converts an AXT formatted file to LAV format' title: AXT to LAV 1.0.0 url: https://usegalaxy.org.au/root?tool_id=axt_to_lav_1 + - description: 'Convert SMILES to MOL: ' + title: Convert SMILES to MOL 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_SMILES_to_MOL + - description: 'Convert compressed file to uncompressed.: ' + title: Convert compressed file to uncompressed. 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gz_to_uncompressed + - description: 'Convert tabular to dbnsfp: ' + title: Convert tabular to dbnsfp 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=tabular_to_dbnsfp + - description: 'Convert Genomic Intervals To Strict BED12: ' + title: Convert Genomic Intervals To Strict BED12 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed12_0 + - description: 'Convert uncompressed file to compressed: ' + title: Convert uncompressed file to compressed 1.16+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_uncompressed_to_gz + - description: 'Convert InChI to MOL: ' + title: Convert InChI to MOL 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_inchi_to_mol + - description: 'OpenBabel converter for molecular formats: ' + title: OpenBabel converter for molecular formats 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_molecules + - description: 'Convert GFF to BED: ' + title: Convert GFF to BED 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_bed_0 + - description: 'Convert BAM to BigWig: ' + title: Convert BAM to BigWig 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_bigwig_0 + - description: 'Convert BAM to queryname-sorted BAM: ' + title: Convert BAM to queryname-sorted BAM 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_qname_sorted_bam + - description: 'Convert FASTQ files to seek locations: ' + title: Convert FASTQ files to seek locations 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fastq_to_fqtoc0 + - description: 'Convert MAF to Genomic Intervals: ' + title: Convert MAF to Genomic Intervals 1.0.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_interval_0 + - description: 'Convert Wiggle to Interval: ' + title: Convert Wiggle to Interval 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wiggle_to_interval_0 + - description: 'Convert Interval to tabix: ' + title: Convert Interval to tabix 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_tabix_0 + - description: 'Convert Ref taxonomy to Seq Taxonomy: converts 2 or 3 column sequence + taxonomy file to a 2 column mothur taxonomy_outline format' + title: Convert Ref taxonomy to Seq Taxonomy 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_ref_to_seq_taxomony + - description: 'Convert BED to Feature Location Index: ' + title: Convert BED to Feature Location Index 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_fli_0 + - description: 'Convert XTC, DCD, and TRR: ' + title: Convert XTC, DCD, and TRR 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mdconvert + - description: 'Convert Genomic Intervals To Strict BED6: ' + title: Convert Genomic Intervals To Strict BED6 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed6_0 + - description: 'Convert plink pbed to linkage lped: ' + title: Convert plink pbed to linkage lped 0.02 + url: https://usegalaxy.org.au/root?tool_id=pbed2lpedconvert + - description: 'Convert tar to directory: ' + title: Convert tar to directory 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_tar_to_directory + - description: 'Convert tabular to CSV: ' + title: Convert tabular to CSV 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=tabular_to_csv + - description: 'Convert Interval to BGZIP: ' + title: Convert Interval to BGZIP 1.0.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bgzip_0 + - description: 'Convert FASTA to len file: ' + title: Convert FASTA to len file 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_len + - description: 'Convert GFF to Feature Location Index: ' + title: Convert GFF to Feature Location Index 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_fli_0 + - description: 'Convert GFF to Interval Index: ' + title: Convert GFF to Interval Index 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_interval_index_0 + - description: 'Convert FASTA to fai file: ' + title: Convert FASTA to fai file 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_fai + - description: 'Convert compressed file to uncompressed.: ' + title: Convert compressed file to uncompressed. 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bz2_to_uncompressed + - description: 'Convert CSV to tabular: ' + title: Convert CSV to tabular 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=csv_to_tabular + - description: 'Convert neostore.zip files to neostore: ' + title: Convert neostore.zip files to neostore 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_neostorezip_to_neostore + - description: 'Convert FASTA to 2bit: ' + title: Convert FASTA to 2bit 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_2bit + - description: 'Convert BGZ VCF to tabix: ' + title: Convert BGZ VCF to tabix 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0 + - description: 'Convert Biom datasets: ' + title: Convert Biom datasets 2.1.5 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_biom + - description: 'Convert FASTA to Bowtie base space Index: ' + title: Convert FASTA to Bowtie base space Index 1.3.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_base_index + - description: 'Convert compressed and uncompressed BCF files: ' + title: Convert compressed and uncompressed BCF files 0.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf + - description: 'Convert Bam to Bai: ' + title: Convert Bam to Bai 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Bam_Bai_0 + - description: 'Convert BED, GFF, or VCF to BigWig: ' + title: Convert BED, GFF, or VCF to BigWig 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_gff_or_vcf_to_bigwig_0 + - description: 'SMILES to SMILES: ' + title: SMILES to SMILES 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_smiles_to_smiles + - description: 'Convert PDB to GRO: ' + title: Convert PDB to GRO 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Pdb_to_Gro_0 + - description: 'Convert FASTA to Bowtie color space Index: ' + title: Convert FASTA to Bowtie color space Index 1.2.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_color_index + - description: 'Convert BED to GFF: ' + title: Convert BED to GFF 2.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_gff_0 + - description: 'Convert Len file to Linecount: ' + title: Convert Len file to Linecount 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_len_to_linecount + - description: 'Convert Picard Interval List to BED6: converter' + title: Convert Picard Interval List to BED6 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_picard_interval_list_to_bed6 + - description: 'Convert FASTA to Tabular: ' + title: Convert FASTA to Tabular 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_tabular + - description: 'Convert MAF to Fasta: ' + title: Convert MAF to Fasta 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_fasta_0 + - description: 'Convert BedGraph to BigWig: ' + title: Convert BedGraph to BigWig 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bedgraph_to_bigwig + - description: 'Convert Parquet to csv: ' + title: Convert Parquet to csv 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_parquet_to_csv + - description: 'Convert SAM to BAM without sorting: ' + title: Convert SAM to BAM without sorting 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_unsorted_bam + - description: 'Convert BigWig to Wiggle: Convert bigWig to wig' + title: Convert BigWig to Wiggle 377+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=bigwigtowig + - description: 'Convert Genomic Intervals To BED: ' + title: Convert Genomic Intervals To BED 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed_0 + - description: 'Convert SAM to BigWig: ' + title: Convert SAM to BigWig 1.0.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_bigwig_0 + - description: 'Convert plink pbed to ld reduced format: ' + title: Convert plink pbed to ld reduced format 0.02 + url: https://usegalaxy.org.au/root?tool_id=pbed2ldindepconvert + - description: 'Convert lped to fped: ' + title: Convert lped to fped 0.02 + url: https://usegalaxy.org.au/root?tool_id=lped2fpedconvert + - description: 'Convert MOL2 to MOL: ' + title: Convert MOL2 to MOL 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mol2_to_mol + - description: 'Convert lped to plink pbed: ' + title: Convert lped to plink pbed 0.02 + url: https://usegalaxy.org.au/root?tool_id=lped2pbedconvert + - description: 'Convert Genomic Intervals To Coverage: ' + title: Convert Genomic Intervals To Coverage 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bigwig_0 + - description: 'Convert BAM to coordinate-sorted BAM: ' + title: Convert BAM to coordinate-sorted BAM 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam + - description: 'Convert GRO to PDB: ' + title: Convert GRO to PDB 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Gro_to_Pdb_0 + - description: 'Convert Wiggle to BigWig: ' + title: Convert Wiggle to BigWig 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wig_to_bigwig + - description: 'Convert CRAM to BAM: ' + title: Convert CRAM to BAM 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cram_to_bam_0 + - description: 'Convert Genomic Intervals To Strict BED: ' + title: Convert Genomic Intervals To Strict BED 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bedstrict_0 + - description: 'Convert CML to SMILES: ' + title: Convert CML to SMILES 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cml_to_smiles homepage: '' id: Galaxy CONVERTER license: '' @@ -5888,13 +7332,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Filter FASTA: on the headers and/or the sequences' title: Filter FASTA 2.3 @@ -5928,13 +7374,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Bar chart: for multiple columns' title: Bar chart 1.0.0 @@ -5947,13 +7395,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Gene BED To Exon/Intron/Codon BED: expander' title: Gene BED To Exon/Intron/Codon BED 1.0.0 @@ -5966,13 +7416,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Reverse: columns in a tabular file' title: Reverse 1.8+galaxy0 @@ -5998,13 +7450,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Number lines: ' title: Number lines 9.3+galaxy1 @@ -6087,6 +7541,9 @@ - description: 'Secure Hash / Message Digest: on a dataset' title: Secure Hash / Message Digest 0.0.2 url: https://usegalaxy.org.au/root?tool_id=secure_hash_message_digest + - description: 'Pick parameter value: ' + title: Pick parameter value 0.2.0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpick_value%2Fpick_value%2F0.2.0 homepage: '' id: galaxy_text_manipulation license: '' @@ -6095,13 +7552,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Combine FASTA and QUAL: into FASTQ' title: Combine FASTA and QUAL 1.1.5 @@ -6162,13 +7621,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Categorize Elements: satisfying criteria' title: Categorize Elements 1.0.0 @@ -6193,11 +7654,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: gatk + biotools: gatk bunya: - 4.3.0.0-gcccore-11.3.0-java-11 description: "The Genome Analysis Toolkit (GATK) is a set of bioinformatic tools\ @@ -6206,6 +7667,24 @@ \ whole genome and exome sequencing data. GATK4 expands functionality into copy\ \ number and somatic analyses and offers pipeline scripts for workflows. \n\n\ Version 4 (GATK4) is open-source at https://github.com/broadinstitute/gatk." + edam-operations: + - term: Polymorphism detection + url: http://edamontology.org/operation_3202 + - term: Sequence analysis + url: http://edamontology.org/operation_2403 + - term: Genotyping + url: http://edamontology.org/operation_3196 + - term: Statistical calculation + url: http://edamontology.org/operation_2238 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Genetic variation + url: http://edamontology.org/topic_0199 + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Workflows + url: http://edamontology.org/topic_0769 galaxy: '' homepage: https://software.broadinstitute.org/gatk/ id: gatk @@ -6223,17 +7702,19 @@ - title: 'The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data' url: http://www.ncbi.nlm.nih.gov/pubmed/20644199 - registry-link: gatk - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis - - Genetic variation - - Sequencing - - Workflows + resources: + - title: .nan + url: .nan - biocontainers: gblocks + biotools: gblocks bunya: '' description: Cleaning aligned sequences. + edam-operations: + - term: Sequence alignment analysis + url: http://edamontology.org/operation_0258 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'Gblocks: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis' @@ -6253,12 +7734,11 @@ - title: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis url: https://doi.org/10.1093/oxfordjournals.molbev.a026334 - registry-link: gblocks - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: gcta + biotools: gcta bunya: - 1.94.0beta-gfbf-2022a - 1.94.1--h9ee0642_0 @@ -6266,6 +7746,12 @@ variance explained by genome- or chromosome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits. + edam-operations: + - term: Genetic variation analysis + url: http://edamontology.org/operation_3197 + edam-topics: + - term: GWAS study + url: http://edamontology.org/topic_3517 galaxy: '' homepage: http://cnsgenomics.com/software/gcta/ id: gcta @@ -6277,16 +7763,21 @@ publications: - title: 'GCTA: A tool for genome-wide complex trait analysis' url: https://doi.org/10.1016/j.ajhg.2010.11.011 - registry-link: gcta - resource-description: .nan - resource-documentation: .nan - topics: - - GWAS study + resources: + - title: .nan + url: .nan - biocontainers: gecko + biotools: gecko bunya: '' description: Software aimed at pairwise sequence comparison generating high quality results (equivalent to MUMmer) with controlled memory consumption and comparable or faster execution times particularly with long sequences. + edam-operations: + - term: Sequence analysis + url: http://edamontology.org/operation_2403 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'Gecko: Ungapped genome comparison' title: Gecko 1.2 @@ -6301,12 +7792,11 @@ publications: - title: Breaking the computational barriers of pairwise genome comparison url: https://doi.org/10.1186/s12859-015-0679-9 - registry-link: gecko - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: gemini + biotools: gemini bunya: '' description: GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the @@ -6314,6 +7804,14 @@ well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. + edam-operations: + - term: Sequence analysis + url: http://edamontology.org/operation_2403 + - term: Genetic variation analysis + url: http://edamontology.org/operation_3197 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'GEMINI actionable_mutations: Retrieve genes with actionable somatic mutations via COSMIC and DGIdb' @@ -6404,18 +7902,25 @@ publications: - title: 10.1371/journal.pcbi.1003153 url: https://doi.org/10.1371/journal.pcbi.1003153 - registry-link: gemini - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: gemoma + biotools: gemoma bunya: '' description: Gene Model Mapper is a homology-based gene prediction program. GeMoMa uses the annotation of protein-coding genes in a reference genome to infer the annotation of protein-coding genes in a target genome. Thereby, it utilizes amino acid sequence and intron position conservation. In addition, it allows to incorporate RNA-seq evidence for splice site prediction. + edam-operations: + - term: Genome annotation + url: http://edamontology.org/operation_0362 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Homology modeling + url: http://edamontology.org/topic_2275 galaxy: '' homepage: http://www.jstacs.de/index.php/GeMoMa id: gemoma @@ -6430,15 +7935,15 @@ - title: Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi url: https://doi.org/10.1186/s12859-018-2203-5 - registry-link: gemoma - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Homology modeling + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Stitch Gene blocks: given a set of coding exon intervals' title: Stitch Gene blocks 1.0.1 @@ -6451,13 +7956,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'gene.iobio visualisation: analyses VCFs for single and trio analysis to find causative variants using gene.iobio''s public server' @@ -6471,13 +7978,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Generate count matrix: from individual files' title: Generate count matrix 1.0 @@ -6490,13 +7999,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Generate A Matrix: for using PC and LDA' title: Generate A Matrix 1.0.0 @@ -6509,13 +8020,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: generode @@ -6526,17 +8039,29 @@ - 0.5.1 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: GenomeScope_2.0 + biotools: GenomeScope_2.0 bunya: '' description: Reference-free profiling of polyploid genomes | We have developed GenomeScope 2.0, which applies classical insights from combinatorial theory to establish a detailed mathematical model of how k-mer frequencies will be distributed in heterozygous and polyploid genomes | Average k-mer coverage for polyploid genome | Upload results from running Jellyfish or KMC + edam-operations: + - term: Genotyping + url: http://edamontology.org/operation_3196 + - term: k-mer counting + url: http://edamontology.org/operation_3472 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Mathematics + url: http://edamontology.org/topic_3315 + - term: Mapping + url: http://edamontology.org/topic_0102 galaxy: - description: 'GenomeScope: reference-free genome profiling' title: GenomeScope 2.0+galaxy2 @@ -6553,16 +8078,21 @@ publications: - title: 10.1101/747568 url: https://doi.org/10.1101/747568 - registry-link: GenomeScope_2.0 - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - Mathematics - - Mapping + resources: + - title: .nan + url: .nan - biocontainers: genometools + biotools: genometools bunya: '' description: Free collection of bioinformatics tools for genome informatics. + edam-operations: + - term: Sequence analysis + url: http://edamontology.org/operation_2403 + edam-topics: + - term: Nucleic acid sites, features and motifs + url: http://edamontology.org/topic_3511 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: '' homepage: http://genometools.org/ id: genometools @@ -6576,15 +8106,15 @@ - title: 'Genome tools: A comprehensive software library for efficient processing of structured genome annotations' url: https://doi.org/10.1109/TCBB.2013.68 - registry-link: genometools - resource-description: .nan - resource-documentation: .nan - topics: - - Nucleic acid sites, features and motifs - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Genrich: Detecting sites of genomic enrichment' title: Genrich 0.5+galaxy2 @@ -6597,13 +8127,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Get PDB file: from Protein Data Bank' title: Get PDB file 0.1.0 @@ -6616,21 +8148,43 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: getorganelle + biotools: getorganelle bunya: '' description: 'A fast and versatile toolkit for accurate de novo assembly of organelle genomes. This toolkit assemblies organelle genome from genomic skimming data.' + edam-operations: + - term: De-novo assembly + url: http://edamontology.org/operation_0524 + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: Mapping assembly + url: http://edamontology.org/operation_0523 + - term: Mapping + url: http://edamontology.org/operation_2429 + - term: Sequence trimming + url: http://edamontology.org/operation_3192 + edam-topics: + - term: Cell biology + url: http://edamontology.org/topic_2229 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Whole genome sequencing + url: http://edamontology.org/topic_3673 + - term: Plant biology + url: http://edamontology.org/topic_0780 + - term: Model organisms + url: http://edamontology.org/topic_0621 galaxy: - description: 'Get organelle from reads: ' - title: Get organelle from reads 1.7.7.0+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgetorganelle%2Fget_organelle_from_reads%2F1.7.7.0%2Bgalaxy1 + title: Get organelle from reads 1.7.7.1+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgetorganelle%2Fget_organelle_from_reads%2F1.7.7.1%2Bgalaxy0 homepage: https://github.com/Kinggerm/GetOrganelle id: getorganelle license: GPL-3.0 @@ -6642,18 +8196,15 @@ - title: 'GetOrganelle: A fast and versatile toolkit for accurate de novo assembly of organelle genomes' url: https://doi.org/10.1186/S13059-020-02154-5 - registry-link: getorganelle - resource-description: .nan - resource-documentation: .nan - topics: - - Cell biology - - Sequence assembly - - Whole genome sequencing - - Plant biology - - Model organisms + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'GFA to FASTA: Convert Graphical Fragment Assembly files to FASTA format' @@ -6667,15 +8218,21 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: gfastats + biotools: gfastats bunya: '' description: gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + edam-topics: + - term: Computational biology + url: http://edamontology.org/topic_3307 galaxy: - description: 'gfastats: the swiss army knife for genome assembly' title: gfastats 1.3.6+galaxy0 @@ -6689,14 +8246,15 @@ - 1.3.6 pawsey: '' publications: '' - registry-link: gfastats - resource-description: .nan - resource-documentation: .nan - topics: - - Computational biology + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'GFF-to-BED: converter' title: GFF-to-BED 1.0.1 @@ -6709,14 +8267,16 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 0.1.a1a2bc9--hdfd78af_2 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: gff3sort @@ -6726,15 +8286,23 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: gffcompare + biotools: gffcompare bunya: - 0.12.2-gcc-10.3.0 description: Program for comparing, annotating, merging and tracking transcripts in GFF files. + edam-operations: + - term: Sequence annotation + url: http://edamontology.org/operation_0361 + edam-topics: + - term: Nucleic acids + url: http://edamontology.org/topic_0077 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'GffCompare: compare assembled transcripts to a reference annotation' title: GffCompare 0.12.6+galaxy0 @@ -6747,15 +8315,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: gffcompare - resource-description: .nan - resource-documentation: .nan - topics: - - Nucleic acids - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Convert gffCompare annotated GTF to BED: for StringTie results' title: Convert gffCompare annotated GTF to BED 0.2.1 @@ -6768,14 +8336,22 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: gffread + biotools: gffread bunya: - 0.12.7-gcccore-10.3.0 description: program for filtering, converting and manipulating GFF files + edam-operations: + - term: Sequence annotation + url: http://edamontology.org/operation_0361 + edam-topics: + - term: Nucleic acids + url: http://edamontology.org/topic_0077 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'gffread: Filters and/or converts GFF3/GTF2 records' title: gffread 2.2.1.4+galaxy0 @@ -6789,15 +8365,19 @@ - 0.12.7 pawsey: '' publications: '' - registry-link: gffread - resource-description: .nan - resource-documentation: .nan - topics: - - Nucleic acids - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: ggplot2 + biotools: ggplot2 bunya: '' description: Plotting system for R, based on the grammar of graphics. + edam-operations: + - term: Visualisation + url: http://edamontology.org/operation_0337 + edam-topics: + - term: Data visualisation + url: http://edamontology.org/topic_0092 galaxy: - description: 'heatmap2: ' title: heatmap2 3.1.3.1+galaxy0 @@ -6827,16 +8407,17 @@ publications: - title: 10.1007/978-3-319-24277-4 url: https://doi.org/10.1007/978-3-319-24277-4 - registry-link: ggplot2 - resource-description: .nan - resource-documentation: .nan - topics: - - Data visualisation + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 9.54.0-gcccore-10.3.0 - 9.56.1-gcccore-11.3.0 (D) description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: ghostscript @@ -6846,13 +8427,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'GMAJ: Multiple Alignment Viewer' title: GMAJ 2.0.1 @@ -6865,14 +8448,22 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: gmap + biotools: gmap bunya: - 2023.04.28 description: Genomic Mapping and Alignment Program for mRNA and EST Sequences. + edam-operations: + - term: Genetic mapping + url: http://edamontology.org/operation_0282 + - term: Sequence alignment + url: http://edamontology.org/operation_0292 + edam-topics: + - term: Mapping + url: http://edamontology.org/topic_0102 galaxy: '' homepage: http://research-pub.gene.com/gmap/ id: gmap @@ -6886,12 +8477,11 @@ url: http://www.ncbi.nlm.nih.gov/pubmed/15728110 - title: 10.7490/f1000research.1114334.1 url: https://doi.org/10.7490/f1000research.1114334.1 - registry-link: gmap - resource-description: .nan - resource-documentation: .nan - topics: - - Mapping + resources: + - title: .nan + url: .nan - biocontainers: parallel + biotools: parallel bunya: - 20210622-gcccore-10.3.0 - 20220722-gcccore-11.3.0 (D) @@ -6901,6 +8491,10 @@ a list of hosts, a list of users, a list of URLs, or a list of tables. A job can also be a command that reads from a pipe. GNU parallel can then split the input and pipe it into commands in parallel. + edam-operations: + - term: Splitting + url: http://edamontology.org/operation_3359 + edam-topics: '' galaxy: '' homepage: https://www.gnu.org/software/parallel/ id: parallel @@ -6911,16 +8505,18 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: parallel - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: gsl + biotools: gsl bunya: - 2.7-gcc-10.3.0 - 2.7-gcc-11.3.0 (D) description: The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://www.gnu.org/software/gsl/ id: gsl @@ -6931,11 +8527,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: gsl - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: goenrichment + biotools: goenrichment bunya: '' description: "GOEnrichment is a tool for performing GO enrichment analysis of gene\ \ sets, such as those obtained from RNA-seq or Microarray experiments, to help\ @@ -6947,6 +8543,12 @@ The tool features an optional graph clustering algorithm to reduce the redundancy\ \ in the set of enriched GO terms and simplify its output.\nIt was developed by\ \ the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ci\xEAncia." + edam-operations: + - term: Gene-set enrichment analysis + url: http://edamontology.org/operation_2436 + edam-topics: + - term: Transcriptomics + url: http://edamontology.org/topic_3308 galaxy: - description: 'GOEnrichment: performs GO enrichment analysis of a set of gene products' title: GOEnrichment 2.0.1 @@ -6963,15 +8565,20 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: goenrichment - resource-description: .nan - resource-documentation: .nan - topics: - - Transcriptomics + resources: + - title: .nan + url: .nan - biocontainers: goseq + biotools: goseq bunya: '' description: Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. + edam-operations: + - term: Gene functional annotation + url: http://edamontology.org/operation_3672 + edam-topics: + - term: RNA-Seq + url: http://edamontology.org/topic_3170 galaxy: - description: 'goseq: tests for overrepresented gene categories' title: goseq 1.50.0+galaxy0 @@ -6986,14 +8593,15 @@ publications: - title: 10.1186/gb-2010-11-2-r14 url: https://doi.org/10.1186/gb-2010-11-2-r14 - registry-link: goseq - resource-description: .nan - resource-documentation: .nan - topics: - - RNA-Seq + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'GrameneMart: Central server' title: GrameneMart 1.0.1 @@ -7006,16 +8614,34 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: graphlan + biotools: graphlan bunya: '' description: GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. + edam-operations: + - term: Phylogenetic inference + url: http://edamontology.org/operation_0323 + - term: Phylogenetic tree visualisation + url: http://edamontology.org/operation_0567 + - term: Phylogenetic tree editing + url: http://edamontology.org/operation_0326 + - term: Taxonomic classification + url: http://edamontology.org/operation_3460 + edam-topics: + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Phylogenetics + url: http://edamontology.org/topic_3293 + - term: Phylogenomics + url: http://edamontology.org/topic_0194 + - term: Cladistics + url: http://edamontology.org/topic_3944 galaxy: - description: 'GraPhlAn: to produce graphical output of an input tree' title: GraPhlAn 1.1.3 @@ -7034,15 +8660,11 @@ - title: Compact graphical representation of phylogenetic data and metadata with GraPhlAn url: https://doi.org/10.7717/peerj.1029 - registry-link: graphlan - resource-description: .nan - resource-documentation: .nan - topics: - - Metagenomics - - Phylogenetics - - Phylogenomics - - Cladistics + resources: + - title: .nan + url: .nan - biocontainers: gromacs + biotools: gromacs bunya: - 2021.3-foss-2021a description: Versatile package to perform molecular dynamics, i.e. simulate the @@ -7051,6 +8673,12 @@ acids that have a lot of complicated bonded interactions, but since it is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. + edam-operations: + - term: Molecular dynamics + url: http://edamontology.org/operation_2476 + edam-topics: + - term: Molecular dynamics + url: http://edamontology.org/topic_0176 galaxy: - description: 'Modify/convert and concatate GROMACS trajectories: using trjconv and trjcat' @@ -7136,12 +8764,11 @@ url: https://doi.org/10.1002/jcc.24030 - title: 'More bang for your buck: Improved use of GPU nodes for GROMACS 2018' url: https://doi.org/10.1002/jcc.26011 - registry-link: gromacs - resource-description: .nan - resource-documentation: .nan - topics: - - Molecular dynamics + resources: + - title: .nan + url: .nan - biocontainers: GTDB-Tk + biotools: GTDB-Tk bunya: - 2.0.0-foss-2021a - 2.2.6 @@ -7158,6 +8785,26 @@ metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).' + edam-operations: + - term: Genome alignment + url: http://edamontology.org/operation_3182 + - term: Taxonomic classification + url: http://edamontology.org/operation_3460 + - term: Sequence assembly + url: http://edamontology.org/operation_0310 + - term: Query and retrieval + url: http://edamontology.org/operation_0224 + edam-topics: + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Taxonomy + url: http://edamontology.org/topic_0637 + - term: Phylogenetics + url: http://edamontology.org/topic_3293 + - term: Database management + url: http://edamontology.org/topic_3489 + - term: Proteins + url: http://edamontology.org/topic_0078 galaxy: - description: 'GTDB-Tk Classify genomes: by placement in GTDB reference tree' title: GTDB-Tk Classify genomes 2.3.2+galaxy1 @@ -7172,18 +8819,15 @@ publications: - title: 'GTDB-Tk: A toolkit to classify genomes with the genome taxonomy database' url: https://doi.org/10.1093/BIOINFORMATICS/BTZ848 - registry-link: GTDB-Tk - resource-description: .nan - resource-documentation: .nan - topics: - - Metagenomics - - Taxonomy - - Phylogenetics - - Database management - - Proteins + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'GTF-to-BEDGraph: converter' title: GTF-to-BEDGraph 1.0.0 @@ -7196,13 +8840,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'GTF2GeneList: extracts a complete annotation table or subsets thereof from an Ensembl GTF using rtracklayer' @@ -7216,14 +8862,28 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: gubbins + biotools: gubbins bunya: '' description: Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. + edam-operations: + - term: Genotyping + url: http://edamontology.org/operation_3196 + - term: Phylogenetic inference + url: http://edamontology.org/operation_0323 + - term: Ancestral reconstruction + url: http://edamontology.org/operation_3745 + edam-topics: + - term: Phylogeny + url: http://edamontology.org/topic_0084 + - term: Genotype and phenotype + url: http://edamontology.org/topic_0625 + - term: Whole genome sequencing + url: http://edamontology.org/topic_3673 galaxy: - description: 'Gubbins: Recombination detection in Bacteria' title: Gubbins 3.2.1+galaxy0 @@ -7238,18 +8898,17 @@ publications: - title: 10.1093/nar/gku1196 url: https://doi.org/10.1093/nar/gku1196 - registry-link: gubbins - resource-description: .nan - resource-documentation: .nan - topics: - - Phylogeny - - Genotype and phenotype - - Whole genome sequencing + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 1.10-gcccore-10.3.0 - 1.12-gcccore-11.3.0 (D) description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Compress file(s): ' title: Compress file(s) 0.1.0 @@ -7262,17 +8921,23 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: hapcut2 + biotools: hapcut2 bunya: '' description: 'HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy across a range of long- and short-read sequencing technologies. The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md' + edam-operations: + - term: Haplotype mapping + url: http://edamontology.org/operation_0487 + - term: Variant classification + url: http://edamontology.org/operation_3225 + edam-topics: '' galaxy: - description: 'Hapcut2: - haplotype assembly for diploid organisms' title: Hapcut2 1.3.3+galaxy0+ga1 @@ -7285,13 +8950,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: hapcut2 - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'HbVar: Human Hemoglobin Variants and Thalassemias' title: HbVar 2.0.0 @@ -7304,13 +8971,23 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: heinz + biotools: heinz bunya: '' description: Tool for single-species active module discovery. + edam-operations: + - term: Pathway or network analysis + url: http://edamontology.org/operation_2497 + edam-topics: + - term: Genetics + url: http://edamontology.org/topic_3053 + - term: Gene expression + url: http://edamontology.org/topic_0203 + - term: Molecular interactions, pathways and networks + url: http://edamontology.org/topic_0602 galaxy: - description: 'Calculate a Heinz score: for each node' title: Calculate a Heinz score 1.0 @@ -7335,17 +9012,26 @@ - title: 'XHeinz: An algorithm for mining cross-species network modules under a flexible conservation model' url: http://www.ncbi.nlm.nih.gov/pubmed/26023104 - registry-link: heinz - resource-description: .nan - resource-documentation: .nan - topics: - - Genetics - - Gene expression - - Molecular interactions, pathways and networks + resources: + - title: .nan + url: .nan - biocontainers: hgv_david + biotools: hgv_david bunya: '' description: This tool provides functional annotation for a list of genes by connecting with DAVID database. + edam-operations: + - term: Database search + url: http://edamontology.org/operation_2421 + - term: Service invocation + url: http://edamontology.org/operation_3763 + - term: Gene functional annotation + url: http://edamontology.org/operation_3672 + edam-topics: + - term: Ontology and terminology + url: http://edamontology.org/topic_0089 + - term: Gene expression + url: http://edamontology.org/topic_0203 galaxy: - description: 'DAVID: functional annotation for a list of genes' title: DAVID 1.0.1 @@ -7366,16 +9052,30 @@ url: https://doi.org/10.1093/nar/gkw343 - title: 10.7490/f1000research.1114334.1 url: https://doi.org/10.7490/f1000research.1114334.1 - registry-link: hgv_david - resource-description: .nan - resource-documentation: .nan - topics: - - Ontology and terminology - - Gene expression + resources: + - title: .nan + url: .nan - biocontainers: hgv_ldtools + biotools: hgv_ldtools bunya: '' description: This tool can be used to analyze the patterns of linkage disequilibrium (LD) between polymorphic sites in a locus. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + - term: Linkage disequilibrium calculation + url: http://edamontology.org/operation_0488 + - term: Variant pattern analysis + url: http://edamontology.org/operation_3504 + edam-topics: + - term: Mapping + url: http://edamontology.org/topic_0102 + - term: Molecular interactions, pathways and networks + url: http://edamontology.org/topic_0602 + - term: DNA polymorphism + url: http://edamontology.org/topic_2885 + - term: Data mining + url: http://edamontology.org/topic_3473 galaxy: - description: 'LD: linkage disequilibrium and tag SNPs' title: LD 1.0.0 @@ -7396,18 +9096,28 @@ url: https://doi.org/10.1093/nar/gkw343 - title: 10.7490/f1000research.1114334.1 url: https://doi.org/10.7490/f1000research.1114334.1 - registry-link: hgv_ldtools - resource-description: .nan - resource-documentation: .nan - topics: - - Mapping - - Molecular interactions, pathways and networks - - DNA polymorphism - - Data mining + resources: + - title: .nan + url: .nan - biocontainers: hgv_linktogprofile + biotools: hgv_linktogprofile bunya: '' description: This tool creates a link to the g:GOSt tool (Gene Group Functional Profiling), which provides functional profiling of gene lists. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + - term: Service invocation + url: http://edamontology.org/operation_3763 + - term: Gene functional annotation + url: http://edamontology.org/operation_3672 + edam-topics: + - term: Ontology and terminology + url: http://edamontology.org/topic_0089 + - term: Function analysis + url: http://edamontology.org/topic_1775 + - term: Data mining + url: http://edamontology.org/topic_3473 galaxy: - description: 'g:Profiler: tools for functional profiling of gene lists' title: g:Profiler 1.0.0 @@ -7428,19 +9138,34 @@ url: https://doi.org/10.1093/nar/gkw343 - title: 10.7490/f1000research.1114334.1 url: https://doi.org/10.7490/f1000research.1114334.1 - registry-link: hgv_linktogprofile - resource-description: .nan - resource-documentation: .nan - topics: - - Ontology and terminology - - Function analysis - - Data mining + resources: + - title: .nan + url: .nan - biocontainers: hicexplorer + biotools: hicexplorer bunya: '' description: "A web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C\ \ data analysis, quality control and visualization.\n\nHiCExplorer \u2014 HiCExplorer\ \ 3.6 documentation.\n\nscHiCExplorer \u2014 scHiCExplorer 7 documentation.\n\n\ Free document hosting provided by Read the Docs." + edam-operations: + - term: Validation + url: http://edamontology.org/operation_2428 + - term: Visualisation + url: http://edamontology.org/operation_0337 + - term: Standardisation and normalisation + url: http://edamontology.org/operation_3435 + edam-topics: + - term: Workflows + url: http://edamontology.org/topic_0769 + - term: DNA + url: http://edamontology.org/topic_0654 + - term: Chromosome conformation capture + url: http://edamontology.org/topic_3940 + - term: ChIP-seq + url: http://edamontology.org/topic_3169 + - term: Epigenetics + url: http://edamontology.org/topic_3295 galaxy: - description: 'hicPCA: compute the principal components for A / B compartment analysis' title: hicPCA 3.7.2+galaxy0 @@ -7470,19 +9195,32 @@ - title: 'Galaxy HiCExplorer 3: A web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization' url: https://doi.org/10.1093/NAR/GKAA220 - registry-link: hicexplorer - resource-description: .nan - resource-documentation: .nan - topics: - - Workflows - - DNA - - Chromosome conformation capture - - ChIP-seq - - Epigenetics + resources: + - title: .nan + url: .nan - biocontainers: hifiadapterfilt + biotools: hifiadapterfilt bunya: '' description: Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz). + edam-operations: + - term: Primer removal + url: http://edamontology.org/operation_3237 + - term: De-novo assembly + url: http://edamontology.org/operation_0524 + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: Sequence trimming + url: http://edamontology.org/operation_3192 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Agricultural science + url: http://edamontology.org/topic_3810 + - term: Workflows + url: http://edamontology.org/topic_0769 + - term: Whole genome sequencing + url: http://edamontology.org/topic_3673 galaxy: - description: 'HiFi Adapter Filter: Remove CCS reads with remnant PacBio adapter sequences' @@ -7501,18 +9239,22 @@ occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly url: https://doi.org/10.1186/s12864-022-08375-1 - registry-link: hifiadapterfilt - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - Agricultural science - - Workflows - - Whole genome sequencing + resources: + - title: .nan + url: .nan - biocontainers: hifiasm + biotools: hifiasm bunya: - 0.16.1-gcccore-10.3.0 description: 'Hifiasm: a haplotype-resolved assembler for accurate Hifi reads' + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: De-novo assembly + url: http://edamontology.org/operation_0524 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: - description: 'Hifiasm: haplotype-resolved de novo assembler for PacBio Hifi reads' title: Hifiasm 0.19.8+galaxy1 @@ -7526,18 +9268,21 @@ - 0.16.1 - 0.18.9 - 0.19.6 + - 0.19.8 + - 0.19.9 pawsey: '' publications: - title: Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm url: https://doi.org/10.1038/s41592-020-01056-5 - registry-link: hifiasm - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Hifiasm_meta: for metagenome assembly using Hifi reads' title: Hifiasm_meta 0.3.1+galaxy0 @@ -7550,11 +9295,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: hisat2 + biotools: hisat2 bunya: - 2.2.1-gompi-2021a - 2.2.1-gompi-2022a @@ -7562,6 +9307,12 @@ description: Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). + edam-operations: + - term: Sequence alignment + url: http://edamontology.org/operation_0292 + edam-topics: + - term: RNA-seq + url: http://edamontology.org/topic_3170 galaxy: - description: 'HISAT2: A fast and sensitive alignment program' title: HISAT2 2.2.1+galaxy1 @@ -7582,14 +9333,15 @@ url: https://doi.org/10.1038/nprot.2016.095 - title: Simulation-based comprehensive benchmarking of RNA-seq aligners url: https://doi.org/10.1038/nmeth.4106 - registry-link: hisat2 - resource-description: .nan - resource-documentation: .nan - topics: - - RNA-seq + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Histogram: of a numeric column' title: Histogram 1.0.4 @@ -7602,13 +9354,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: hmmcleaner @@ -7619,11 +9373,11 @@ - '0.180750' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: hmmer3 + biotools: hmmer3 bunya: - 3.3.2-gompi-2021a - 3.3.2-gompi-2022a (D) @@ -7631,6 +9385,16 @@ protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. + edam-operations: + - term: Formatting + url: http://edamontology.org/operation_0335 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Sequence sites, features and motifs + url: http://edamontology.org/topic_0160 + - term: Gene and protein families + url: http://edamontology.org/topic_0623 galaxy: - description: 'hmmconvert: convert profile file to a HMMER format' title: hmmconvert 0.1.0 @@ -7687,18 +9451,19 @@ url: https://doi.org/10.1093/nar/gkt263 - title: 'HMMER web server: 2018 update' url: https://doi.org/10.1093/nar/gky448 - registry-link: hmmer3 - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis - - Sequence sites, features and motifs - - Gene and protein families + resources: + - title: .nan + url: .nan - biocontainers: horovod + biotools: horovod bunya: '' description: Horovod is a distributed deep learning training framework for TensorFlow, Keras, PyTorch, and Apache MXNet. The goal of Horovod is to make distributed deep learning fast and easy to use. + edam-operations: '' + edam-topics: + - term: Machine learning + url: http://edamontology.org/topic_3474 galaxy: '' homepage: https://github.com/horovod/horovod id: horovod @@ -7710,16 +9475,21 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: horovod - resource-description: .nan - resource-documentation: .nan - topics: - - Machine learning + resources: + - title: .nan + url: .nan - biocontainers: htseq + biotools: htseq bunya: - 2.0.2-foss-2022a description: Python framework to process and analyse high-throughput sequencing (HTS) data + edam-operations: + - term: Nucleic acid sequence analysis + url: http://edamontology.org/operation_2478 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'htseq-count: - Count aligned reads in a BAM file that overlap features in a GFF file' @@ -7735,12 +9505,11 @@ publications: - title: HTSeq-A Python framework to work with high-throughput sequencing data url: https://doi.org/10.1093/bioinformatics/btu638 - registry-link: htseq - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: htslib + biotools: htslib bunya: - 1.12-gcc-10.3.0 - 1.15.1-gcc-11.3.0 (D) @@ -7749,6 +9518,12 @@ and BCF formats). The library also provides interfaces to access and index genome reference data in FASTA format and tab-delimited files with genomic coordinates. It is utilized and incorporated into both SAMtools and BCFtools. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + edam-topics: + - term: Data management + url: http://edamontology.org/topic_3071 galaxy: '' homepage: http://www.htslib.org/ id: htslib @@ -7758,17 +9533,17 @@ - '1.9' - '1.12' - '1.16' - nci-if89: '' + nci-if89: + - 1.19.1 pawsey: '' publications: - title: 'HTSlib: C library for reading/writing high-Throughput sequencing data' url: https://doi.org/10.1093/gigascience/giab007 - registry-link: htslib - resource-description: .nan - resource-documentation: .nan - topics: - - Data management + resources: + - title: .nan + url: .nan - biocontainers: humann + biotools: humann bunya: - 3.6-foss-2022a description: "HUMAnN is a pipeline for efficiently and accurately profiling the\ @@ -7778,6 +9553,18 @@ \ potential of a microbial community and its members. More generally, functional\ \ profiling answers the question \u201CWhat are the microbes in my community-of-interest\ \ doing (or are capable of doing)?\u201D" + edam-operations: + - term: Species frequency estimation + url: http://edamontology.org/operation_3221 + - term: Taxonomic classification + url: http://edamontology.org/operation_3460 + - term: Phylogenetic analysis + url: http://edamontology.org/operation_0324 + edam-topics: + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Phylogenomics + url: http://edamontology.org/topic_0194 galaxy: - description: 'Join (merge): gene, pathway, or taxonomy HUMAnN/MetaPhlAn tables into a single table' @@ -7828,13 +9615,11 @@ - title: Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with biobakery 3 url: https://doi.org/10.7554/eLife.65088 - registry-link: humann - resource-description: .nan - resource-documentation: .nan - topics: - - Metagenomics - - Phylogenomics + resources: + - title: .nan + url: .nan - biocontainers: humann2 + biotools: humann2 bunya: '' description: "HUMAnN 2.0 is a pipeline for efficiently and accurately profiling\ \ the presence/absence and abundance of microbial pathways in a community from\ @@ -7843,6 +9628,10 @@ \ the metabolic potential of a microbial community and its members. More generally,\ \ functional profiling answers the question \u201CWhat are the microbes in my\ \ community-of-interest doing (or capable of doing)?\u201D" + edam-operations: + - term: Metabolic pathway prediction + url: http://edamontology.org/operation_3929 + edam-topics: '' galaxy: - description: 'HUMAnN2: to profile presence/absence and abundance of microbial pathways and gene families' @@ -7873,13 +9662,15 @@ publications: - title: Species-level functional profiling of metagenomes and metatranscriptomes url: https://doi.org/10.1038/s41592-018-0176-y - registry-link: humann2 - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'HybPiper: Analyse targeted sequence capture data' title: HybPiper 2.1.6+galaxy0 @@ -7892,14 +9683,24 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: HyPhy + biotools: HyPhy bunya: '' description: Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. + edam-operations: + - term: Statistical calculation + url: http://edamontology.org/operation_2238 + edam-topics: + - term: Phylogeny + url: http://edamontology.org/topic_0084 + - term: Small molecules + url: http://edamontology.org/topic_0154 + - term: Molecular interactions, pathways and networks + url: http://edamontology.org/topic_0602 galaxy: - description: 'HyPhy-aBSREL: adaptive Branch Site Random Effects Likelihood' title: HyPhy-aBSREL 2.5.47+galaxy0 @@ -7919,16 +9720,15 @@ url: https://doi.org/10.1007/978-1-4939-8736-8_6 - title: 10.1093/bioinformatics/bti079 url: https://doi.org/10.1093/bioinformatics/bti079 - registry-link: HyPhy - resource-description: .nan - resource-documentation: .nan - topics: - - Phylogeny - - Small molecules - - Molecular interactions, pathways and networks + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://www.l3harrisgeospatial.com/Software-Technology/IDL id: idl @@ -7940,15 +9740,17 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 7.0.11-14-gcccore-10.3.0 - 7.1.0-37-gcccore-11.3.0 (D) description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://imagemagick.org/script/index.php id: imagemagick @@ -7959,15 +9761,23 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: ipa_hifi + biotools: ipa_hifi bunya: '' description: Improved Phased Assembler (IPA) is the official PacBio software for HiFi genome assembly. IPA was designed to utilize the accuracy of PacBio HiFi reads to produce high-quality phased genome assemblies + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: Phasing + url: http://edamontology.org/operation_3454 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: '' homepage: https://github.com/PacificBiosciences/pbipa id: pbipa @@ -7979,12 +9789,11 @@ - 1.8.0 pawsey: '' publications: '' - registry-link: ipa_hifi - resource-description: Install and testing at Pawsey - resource-documentation: https://github.com/AustralianBioCommons/ipa - topics: - - Sequence assembly + resources: + - title: Install and testing at Pawsey + url: https://github.com/AustralianBioCommons/ipa - biocontainers: infernal + biotools: infernal bunya: '' description: Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation @@ -7993,6 +9802,14 @@ sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence. + edam-operations: + - term: Nucleic acid feature detection + url: http://edamontology.org/operation_0415 + edam-topics: + - term: Sequence sites, features and motifs + url: http://edamontology.org/topic_0160 + - term: Structural genomics + url: http://edamontology.org/topic_0122 galaxy: - description: 'cmscan: Search sequences against collections of covariance models' title: cmscan 1.1.4+galaxy0 @@ -8023,15 +9840,15 @@ publications: - title: 'Infernal 1.1: 100-fold faster RNA homology searches' url: https://doi.org/10.1093/bioinformatics/btt509 - registry-link: infernal - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence sites, features and motifs - - Structural genomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: insight-toolkit @@ -8042,16 +9859,26 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: igv + biotools: igv bunya: '' description: High-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types and format, including short-read alignments in the SAM/BAM format. Data can be viewed from local files or over the web via http. + edam-operations: + - term: Visualisation + url: http://edamontology.org/operation_0337 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Data visualisation + url: http://edamontology.org/topic_0092 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: '' homepage: http://www.broadinstitute.org/igv/ id: igv @@ -8070,16 +9897,31 @@ - title: 'igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV)' url: https://doi.org/10.1093/BIOINFORMATICS/BTAC830 - registry-link: igv - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Data visualisation - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: integron_finder + biotools: integron_finder bunya: '' description: A tool to detect Integron in DNA sequences. + edam-operations: + - term: Nucleic acid feature detection + url: http://edamontology.org/operation_0415 + - term: Sequence motif recognition + url: http://edamontology.org/operation_0239 + - term: Protein feature detection + url: http://edamontology.org/operation_3092 + - term: Genome annotation + url: http://edamontology.org/operation_0362 + edam-topics: + - term: Functional genomics + url: http://edamontology.org/topic_0085 + - term: Mobile genetic elements + url: http://edamontology.org/topic_0798 + - term: Molecular biology + url: http://edamontology.org/topic_3047 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'Integron Finder: is a program that detects integrons in DNA sequences' title: Integron Finder 2.0.3+galaxy0 @@ -8098,17 +9940,15 @@ - title: 'Integron Functionality and Genome Innovation: An Update on the Subtle and Smart Strategy of Integrase and Gene Cassette Expression Regulation' url: https://doi.org/10.3390/microorganisms10020224 - registry-link: integron_finder - resource-description: .nan - resource-documentation: .nan - topics: - - Functional genomics - - Mobile genetic elements - - Molecular biology - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'InterMine: server' title: InterMine 1.0.0 @@ -8121,13 +9961,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Create InterMine Interchange: Dataset' title: Create InterMine Interchange 0.0.1 @@ -8140,14 +9982,24 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: interproscan_4 + biotools: interproscan_4 bunya: - 5.55-88.0-foss-2021a description: Scan sequences against the InterPro protein signature databases. + edam-operations: + - term: Sequence motif recognition + url: http://edamontology.org/operation_0239 + - term: Protein feature detection + url: http://edamontology.org/operation_3092 + edam-topics: + - term: Gene and protein families + url: http://edamontology.org/topic_0623 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'InterProScan: functional annotation' title: InterProScan 5.59-91.0+galaxy3 @@ -8164,15 +10016,15 @@ url: https://doi.org/10.1093/bioinformatics/btu031 - title: Search and sequence analysis tools services from EMBL-EBI in 2022 url: https://doi.org/10.1093/nar/gkac240 - registry-link: interproscan_4 - resource-description: .nan - resource-documentation: .nan - topics: - - Gene and protein families - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Stitch MAF blocks: given a set of genomic intervals' title: Stitch MAF blocks 1.0.1 @@ -8185,13 +10037,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Extract Pairwise MAF blocks: given a set of genomic intervals' title: Extract Pairwise MAF blocks 1.0.1 @@ -8204,13 +10058,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Extract MAF blocks: given a set of genomic intervals' title: Extract MAF blocks 1.0.1 @@ -8223,11 +10079,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: ipyrad + biotools: ipyrad bunya: - 0.9.93 description: "Interactive assembly and analysis of RADseq datasets.\n\nipyrad: interactive\ @@ -8235,6 +10091,20 @@ \ toolkit for assembly and analysis of restriction-site associated genomic data\ \ sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies.\n\ \nWelcome to ipyrad \u2014 ipyrad documentation." + edam-operations: + - term: Sequence assembly + url: http://edamontology.org/operation_0310 + - term: de Novo sequencing + url: http://edamontology.org/operation_3644 + - term: Haplotype mapping + url: http://edamontology.org/operation_0487 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Phylogenetics + url: http://edamontology.org/topic_3293 + - term: Population genetics + url: http://edamontology.org/topic_3056 galaxy: '' homepage: https://github.com/dereneaton/ipyrad/ id: ipyrad @@ -8247,25 +10117,32 @@ publications: - title: 'Ipyrad: Interactive assembly and analysis of RADseq datasets' url: https://doi.org/10.1093/BIOINFORMATICS/BTZ966 - registry-link: ipyrad - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - Phylogenetics - - Population genetics + resources: + - title: .nan + url: .nan - biocontainers: iq-tree + biotools: iq-tree bunya: - 2.2.2.3--h2202e69_2 description: Very efficient phylogenetic software for reconstructing maximum-likelihood trees and assessing branch supports with the ultrafast bootstrap approximation. It is based on the IQPNNI algorithm with 10-fold speedup together with substantially additional features. + edam-operations: + - term: Phylogenetic tree generation (maximum likelihood and Bayesian methods) + url: http://edamontology.org/operation_0547 + edam-topics: + - term: Phylogenetics + url: http://edamontology.org/topic_3293 + - term: Statistics and probability + url: http://edamontology.org/topic_2269 + - term: Phylogenomics + url: http://edamontology.org/topic_0194 galaxy: - description: 'IQ-TREE: Phylogenomic / evolutionary tree construction from multiple sequences' - title: IQ-TREE 2.1.2+galaxy2 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fiqtree%2Fiqtree%2F2.1.2%2Bgalaxy2 + title: IQ-TREE 2.3.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fiqtree%2Fiqtree%2F2.3.3%2Bgalaxy0 homepage: http://www.cibiv.at/software/iqtree/ id: iq-tree license: '' @@ -8277,20 +10154,25 @@ publications: - title: 'W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis' url: http://www.ncbi.nlm.nih.gov/pubmed/27084950 - registry-link: iq-tree - resource-description: .nan - resource-documentation: .nan - topics: - - Phylogenetics - - Statistics and probability - - Phylogenomics + resources: + - title: .nan + url: .nan - biocontainers: isee + biotools: isee bunya: '' description: Provides functions for creating an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. Particular attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results. + edam-operations: + - term: Clustering + url: http://edamontology.org/operation_3432 + edam-topics: + - term: Gene expression + url: http://edamontology.org/topic_0203 + - term: Transcriptomics + url: http://edamontology.org/topic_3308 galaxy: - description: 'iSEE: ' title: iSEE 1.0.0 @@ -8306,16 +10188,26 @@ - title: 'iSEE: Interactive SummarizedExperiment Explorer [version 1; referees: 2 approved]' url: https://doi.org/10.12688/f1000research.14966.1 - registry-link: isee - resource-description: .nan - resource-documentation: .nan - topics: - - Gene expression - - Transcriptomics + resources: + - title: .nan + url: .nan - biocontainers: isescan + biotools: isescan bunya: '' description: Automated identification of insertion sequence elements in prokaryotic genomes. + edam-operations: + - term: Structural variation detection + url: http://edamontology.org/operation_3228 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: DNA structural variation + url: http://edamontology.org/topic_3175 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Genetic variation + url: http://edamontology.org/topic_0199 galaxy: - description: 'ISEScan: Insertion Sequence Elements detection in prokaryotic genomes' title: ISEScan 1.7.2.3+galaxy1 @@ -8331,21 +10223,27 @@ - title: 'ISEScan: automated identification of insertion sequence elements in prokaryotic genomes' url: https://doi.org/10.1093/bioinformatics/btx433 - registry-link: isescan - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - DNA structural variation - - Sequence analysis - - Genetic variation + resources: + - title: .nan + url: .nan - biocontainers: isoformswitchanalyzer + biotools: isoformswitchanalyzer bunya: '' description: Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. + edam-operations: + - term: Sequence comparison + url: http://edamontology.org/operation_2451 + - term: Sequence analysis + url: http://edamontology.org/operation_2403 + edam-topics: + - term: Computational biology + url: http://edamontology.org/topic_3307 + - term: Gene transcripts + url: http://edamontology.org/topic_3512 galaxy: - description: 'IsoformSwitchAnalyzeR: statistical identification of isoform switching' title: IsoformSwitchAnalyzeR 1.20.0+galaxy5 @@ -8360,19 +10258,31 @@ publications: - title: The landscape of isoform switches in human cancers url: https://doi.org/10.1158/1541-7786.MCR-16-0459 - registry-link: isoformswitchanalyzer - resource-description: .nan - resource-documentation: .nan - topics: - - Computational biology - - Gene transcripts + resources: + - title: .nan + url: .nan - biocontainers: isoseq3 + biotools: isoseq3 bunya: - 4.0.0--h9ee0642_0 description: IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique. + edam-operations: + - term: Demultiplexing + url: http://edamontology.org/operation_3933 + - term: Sequence trimming + url: http://edamontology.org/operation_3192 + - term: Clustering + url: http://edamontology.org/operation_3432 + - term: Primer removal + url: http://edamontology.org/operation_3237 + - term: DNA barcoding + url: http://edamontology.org/operation_3200 + edam-topics: + - term: Gene transcripts + url: http://edamontology.org/topic_3512 galaxy: '' homepage: https://github.com/PacificBiosciences/IsoSeq id: isoseq3 @@ -8382,18 +10292,31 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: isoseq3 - resource-description: .nan - resource-documentation: .nan - topics: - - Gene transcripts + resources: + - title: .nan + url: .nan - biocontainers: ivar + biotools: ivar bunya: '' description: 'Interpretation-oriented tool to manage the update and revision of variant annotation and classification. iVar - DataBase of Genomics Variants.' + edam-operations: + - term: Variant classification + url: http://edamontology.org/operation_3225 + - term: Text annotation + url: http://edamontology.org/operation_3778 + - term: Variant calling + url: http://edamontology.org/operation_3227 + edam-topics: + - term: Biological databases + url: http://edamontology.org/topic_3071 + - term: Evolutionary biology + url: http://edamontology.org/topic_3299 + - term: Sequencing + url: http://edamontology.org/topic_3168 galaxy: - description: 'ivar consensus: Call consensus from aligned BAM file' title: ivar consensus 1.4.2+galaxy0 @@ -8425,19 +10348,22 @@ publications: - title: 10.22541/AU.160610419.99549785/V1 url: https://doi.org/10.22541/AU.160610419.99549785/V1 - registry-link: ivar - resource-description: .nan - resource-documentation: .nan - topics: - - Biological databases - - Evolutionary biology - - Sequencing + resources: + - title: .nan + url: .nan - biocontainers: iwtomics + biotools: iwtomics bunya: '' description: Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset. + edam-operations: + - term: Differential gene expression analysis + url: http://edamontology.org/operation_3223 + edam-topics: + - term: Statistics and probability + url: http://edamontology.org/topic_2269 galaxy: - description: 'IWTomics Load: Smooth and Plot' title: IWTomics Load 1.0.0.0 @@ -8459,16 +10385,19 @@ - title: 'IWTomics: Testing high-resolution sequence-based ''Omics'' data at multiple locations and scales' url: https://doi.org/10.1093/bioinformatics/bty090 - registry-link: iwtomics - resource-description: .nan - resource-documentation: .nan - topics: - - Statistics and probability + resources: + - title: .nan + url: .nan - biocontainers: jags + biotools: jags bunya: - 4.3.0-foss-2021a description: JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation. + edam-operations: '' + edam-topics: + - term: Statistics and probability + url: http://edamontology.org/topic_2269 galaxy: '' homepage: https://mcmc-jags.sourceforge.io/ id: jags @@ -8478,12 +10407,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: jags - resource-description: .nan - resource-documentation: .nan - topics: - - Statistics and probability + resources: + - title: .nan + url: .nan - biocontainers: jasmine-sv + biotools: jasmine-sv bunya: '' description: JASMINE (Jointly Accurate Sv Merging with Intersample Network Edges) is an automated pipeline for alignment and SV calling in long-read datasets. The @@ -8494,6 +10422,26 @@ forest algorithm to determine the best way of merging the variants such that each merged variants represents a set of analogous variants occurring in different samples. + edam-operations: + - term: Genotyping + url: http://edamontology.org/operation_3196 + - term: Variant calling + url: http://edamontology.org/operation_3227 + - term: Genome indexing + url: http://edamontology.org/operation_3211 + - term: Visualisation + url: http://edamontology.org/operation_0337 + edam-topics: + - term: Structural variation + url: http://edamontology.org/topic_3175 + - term: DNA polymorphism + url: http://edamontology.org/topic_2885 + - term: Workflows + url: http://edamontology.org/topic_0769 + - term: Mapping + url: http://edamontology.org/topic_0102 + - term: RNA-Seq + url: http://edamontology.org/topic_3170 galaxy: '' homepage: https://github.com/mkirsche/Jasmine id: jasminesv @@ -8506,18 +10454,15 @@ publications: - title: 10.1101/2021.05.27.445886 url: https://doi.org/10.1101/2021.05.27.445886 - registry-link: jasmine-sv - resource-description: .nan - resource-documentation: .nan - topics: - - Structural variation - - DNA polymorphism - - Workflows - - Mapping - - RNA-Seq + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: jdk @@ -8528,15 +10473,17 @@ - 11.0.2 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 2.1-gcccore-10.3.0 - 2.1-gcccore-11.3.0 (D) description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: jbigkit @@ -8546,15 +10493,21 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: jbrowse + biotools: jbrowse bunya: '' description: Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. + edam-operations: + - term: Genome visualisation + url: http://edamontology.org/operation_3208 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: - description: 'JBrowse: genome browser' title: JBrowse 1.16.11+galaxy1 @@ -8573,14 +10526,15 @@ publications: - title: 10.1101/gr.094607.109 url: https://doi.org/10.1101/gr.094607.109 - registry-link: jbrowse - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Genome annotation statistics: ' title: Genome annotation statistics 0.8.4 @@ -8593,15 +10547,23 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: jellyfish + biotools: jellyfish bunya: - 2.3.0-gcc-10.3.0 - 2.3.0-gcc-11.3.0 (D) description: A command-line algorithm for counting k-mers in DNA sequence. + edam-operations: + - term: k-mer counting + url: http://edamontology.org/operation_3472 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: - description: 'jellyfish: ' title: jellyfish 2.3.0+galaxy1 @@ -8617,15 +10579,15 @@ publications: - title: 10.1093/bioinformatics/btr011 url: https://doi.org/10.1093/bioinformatics/btr011 - registry-link: jellyfish - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Join two files: on column allowing a small difference' title: Join two files 1.0.1 @@ -8638,13 +10600,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'JQ: process JSON' title: JQ 1.0 @@ -8657,16 +10621,30 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: juicer + biotools: juicer bunya: - '1.6' description: Juicer is a platform for analyzing kilobase resolution Hi-C data. In this distribution, we include the pipeline for generating Hi-C maps from fastq raw data files and command line tools for feature annotation on the Hi-C maps. + edam-operations: + - term: Genome indexing + url: http://edamontology.org/operation_3211 + - term: Visualisation + url: http://edamontology.org/operation_0337 + edam-topics: + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Mapping + url: http://edamontology.org/topic_0102 + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Epigenetics + url: http://edamontology.org/topic_3295 galaxy: '' homepage: https://github.com/aidenlab/juicer id: juicer @@ -8678,18 +10656,16 @@ publications: - title: Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments url: https://doi.org/10.1016/j.cels.2016.07.002 - registry-link: juicer - resource-description: .nan - resource-documentation: .nan - topics: - - Sequencing - - Mapping - - Genomics - - Epigenetics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 3.5.0-gcccore-11.3.0 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: jupyterlab @@ -8700,11 +10676,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: kallisto + biotools: kallisto bunya: - 0.48.0-gompi-2021a - 0.48.0-gompi-2022a @@ -8713,6 +10689,16 @@ or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. + edam-operations: + - term: Gene expression profiling + url: http://edamontology.org/operation_0314 + edam-topics: + - term: Transcriptomics + url: http://edamontology.org/topic_3308 + - term: RNA-seq + url: http://edamontology.org/topic_3170 + - term: Gene expression + url: http://edamontology.org/topic_0203 galaxy: - description: 'Kallisto pseudo: run pseudoalignment on RNA-Seq transcripts' title: Kallisto pseudo 0.48.0+galaxy1 @@ -8730,17 +10716,24 @@ publications: - title: Near-optimal probabilistic RNA-seq quantification url: https://doi.org/10.1038/nbt.3519 - registry-link: kallisto - resource-description: .nan - resource-documentation: .nan - topics: - - Transcriptomics - - RNA-seq - - Gene expression + resources: + - title: .nan + url: .nan - biocontainers: kat + biotools: kat bunya: '' description: Suite of tools that generate, analyse and compare k-mer spectra produced from sequence files + edam-operations: + - term: Sequence composition calculation + url: http://edamontology.org/operation_0236 + - term: Sequence feature detection + url: http://edamontology.org/operation_0253 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: '' homepage: http://www.earlham.ac.uk/kat-tools id: kat @@ -8754,15 +10747,15 @@ - title: 'KAT: A K-mer analysis toolkit to quality control NGS datasets and genome assemblies' url: https://doi.org/10.1093/bioinformatics/btw663 - registry-link: kat - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://github.com/ucscGenomeBrowser/kent id: kentutils @@ -8773,16 +10766,22 @@ - '0.0' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: khmer + biotools: khmer bunya: '' description: khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. + edam-operations: + - term: Standardisation and normalisation + url: http://edamontology.org/operation_3435 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: - description: 'khmer: Abundance Distribution: Calculate abundance distribution of k-mers using pre-made k-mer countgraphs' @@ -8831,15 +10830,24 @@ url: https://doi.org/10.1371/journal.pone.0101271 - title: 10.7287/peerj.preprints.890v1 url: https://doi.org/10.7287/peerj.preprints.890v1 - registry-link: khmer - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly + resources: + - title: .nan + url: .nan - biocontainers: kmc + biotools: kmc bunya: '' description: KMC is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects. + edam-operations: + - term: k-mer counting + url: http://edamontology.org/operation_3472 + edam-topics: + - term: Whole genome sequencing + url: http://edamontology.org/topic_3673 + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: '' homepage: http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=about id: kmc @@ -8852,17 +10860,16 @@ publications: - title: 'KMC 2: Fast and resource-frugal k-mer counting' url: http://www.ncbi.nlm.nih.gov/pubmed/25609798 - registry-link: kmc - resource-description: .nan - resource-documentation: .nan - topics: - - Whole genome sequencing - - Genomics - - Sequence assembly + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 1.3.0--hdfd78af_2 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: kofamscan @@ -8872,11 +10879,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: kraken + biotools: kraken bunya: '' description: System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics @@ -8885,6 +10892,14 @@ but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. + edam-operations: + - term: Taxonomic classification + url: http://edamontology.org/operation_3460 + edam-topics: + - term: Taxonomy + url: http://edamontology.org/topic_0637 + - term: Metagenomics + url: http://edamontology.org/topic_3174 galaxy: - description: 'Convert Kraken: data to Galaxy taxonomy representation' title: Convert Kraken 1.2+galaxy0 @@ -8924,13 +10939,11 @@ publications: - title: 'Kraken: Ultrafast metagenomic sequence classification using exact alignments' url: https://doi.org/10.1186/gb-2014-15-3-r46 - registry-link: kraken - resource-description: .nan - resource-documentation: .nan - topics: - - Taxonomy - - Metagenomics + resources: + - title: .nan + url: .nan - biocontainers: kraken2 + biotools: kraken2 bunya: - 2.1.2-gompi-2021a - 2.1.2-gompi-2022a (D) @@ -8939,6 +10952,14 @@ speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. + edam-operations: + - term: Taxonomic classification + url: http://edamontology.org/operation_3460 + edam-topics: + - term: Taxonomy + url: http://edamontology.org/topic_0637 + - term: Metagenomics + url: http://edamontology.org/topic_3174 galaxy: - description: 'Kraken2: assign taxonomic labels to sequencing reads' title: Kraken2 2.1.1+galaxy1 @@ -8953,16 +10974,22 @@ publications: - title: 10.1101/762302 url: https://doi.org/10.1101/762302 - registry-link: kraken2 - resource-description: .nan - resource-documentation: .nan - topics: - - Taxonomy - - Metagenomics + resources: + - title: .nan + url: .nan - biocontainers: krakentools + biotools: krakentools bunya: '' description: KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files + edam-operations: + - term: Visualisation + url: http://edamontology.org/operation_0337 + edam-topics: + - term: Taxonomy + url: http://edamontology.org/topic_0637 + - term: Metagenomics + url: http://edamontology.org/topic_3174 galaxy: - description: 'Krakentools: Combine multiple Kraken reports: into a combined report file' @@ -8987,16 +11014,20 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: krakentools - resource-description: .nan - resource-documentation: .nan - topics: - - Taxonomy - - Metagenomics + resources: + - title: .nan + url: .nan - biocontainers: krona + biotools: krona bunya: '' description: Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). + edam-operations: + - term: Visualisation + url: http://edamontology.org/operation_0337 + edam-topics: + - term: Metagenomics + url: http://edamontology.org/topic_3174 galaxy: - description: 'Krona pie chart: from taxonomic profile' title: Krona pie chart 2.7.1+galaxy0 @@ -9014,15 +11045,16 @@ publications: - title: Interactive metagenomic visualization in a Web browser url: http://www.ncbi.nlm.nih.gov/pubmed/21961884 - registry-link: krona - resource-description: .nan - resource-documentation: .nan - topics: - - Metagenomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 2.8.1-gcccore-11.3.0 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: kronatools @@ -9032,11 +11064,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: lama + biotools: lama bunya: '' description: 'Automated image analysis for developmental phenotyping of mouse embryos. @@ -9046,6 +11078,22 @@ Welcome to LAMA, an open source pipeline to automatically identify embryo dysmorphology from 3D volumetric images.' + edam-operations: + - term: Image analysis + url: http://edamontology.org/operation_3443 + - term: Image annotation + url: http://edamontology.org/operation_3553 + - term: Standardisation and normalisation + url: http://edamontology.org/operation_3435 + edam-topics: + - term: Tomography + url: http://edamontology.org/topic_3452 + - term: Genotype and phenotype + url: http://edamontology.org/topic_0625 + - term: MRI + url: http://edamontology.org/topic_3444 + - term: Workflows + url: http://edamontology.org/topic_0769 galaxy: '' homepage: https://github.com/mpi2/LAMA id: lama @@ -9060,18 +11108,22 @@ publications: - title: 10.1101/2020.05.04.075853 url: https://doi.org/10.1101/2020.05.04.075853 - registry-link: lama - resource-description: .nan - resource-documentation: .nan - topics: - - Tomography - - Genotype and phenotype - - MRI - - Workflows + resources: + - title: .nan + url: .nan - biocontainers: lastz + biotools: lastz bunya: '' description: A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. + edam-operations: + - term: Sequence alignment + url: http://edamontology.org/operation_0292 + - term: Read mapping + url: http://edamontology.org/operation_3198 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: - description: 'LASTZ_D: : estimate substitution scores matrix' title: LASTZ_D 1.04.22+galaxy0 @@ -9091,14 +11143,15 @@ - 1.04.15 pawsey: '' publications: '' - registry-link: lastz - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'LAV to BED: Converts a LAV formatted file to BED format' title: LAV to BED 1.0.0 @@ -9111,13 +11164,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Gene length and GC content: from GTF and FASTA file' title: Gene length and GC content 0.1.2 @@ -9130,51 +11185,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' -- biocontainers: LFQ-Analyst - bunya: '' - description: "An Easy-To-Use Interactive Web Platform To Analyze and Visualize Label-Free\ - \ Proteomics Data Preprocessed with MaxQuant.\n\nA tool for analysing label-free\ - \ quantitative proteomics dataset https://bioinformatics.erc.monash.edu/apps/LFQ-Analyst/.\n\ - \nLFQ-Analyst: An easy-to-use interactive web-platform to analyze and visualize\ - \ proteomics data preprocessed with MaxQuant.\n\nLFQ-Analyst is an easy-to-use,\ - \ interactive web application developed to perform differential expression analysis\ - \ with \u201Cone click\u201D and to visualize label-free quantitative proteomic\ - \ datasets preprocessed with MaxQuant. LFQ-Analyst provides a wealth of user-analytic\ - \ features and offers numerous publication-quality result output graphics and\ - \ tables to facilitate statistical and exploratory analysis of label-free quantitative\ - \ datasets" - galaxy: - - description: 'LFQ Analyst: Analyze and Visualize Label-Free Proteomics output - from MaxQuant' - title: LFQ Analyst 1.2.5+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=interactive_tool_lfqanalyst - homepage: https://bioinformatics.erc.monash.edu/apps/LFQ-Analyst - id: LFQ-Analyst - license: GPL-3.0 - name: LFQ-Analyst - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: - - title: 'Lfq-Analyst: An easy-To-use interactive web platform to analyze and visualize - label-free proteomics data preprocessed with maxquant' - url: https://doi.org/10.1021/ACS.JPROTEOME.9B00496 - registry-link: LFQ-Analyst - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics - - Sequence analysis - - Small molecules - - Metabolomics - - Proteomics experiment + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Convert genome coordinates: between assemblies and genomes' title: Convert genome coordinates 1.0.6 @@ -9187,14 +11206,22 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: limma + biotools: limma bunya: '' description: Data analysis, linear models and differential expression for microarray data. + edam-operations: + - term: RNA-Seq analysis + url: http://edamontology.org/operation_3680 + edam-topics: + - term: Molecular biology + url: http://edamontology.org/topic_3047 + - term: Genetics + url: http://edamontology.org/topic_3053 galaxy: - description: 'limma: Perform differential expression with limma-voom or limma-trend' title: limma 3.58.1+galaxy0 @@ -9210,19 +11237,35 @@ - title: Limma powers differential expression analyses for RNA-sequencing and microarray studies url: https://doi.org/10.1093/nar/gkv007 - registry-link: limma - resource-description: .nan - resource-documentation: .nan - topics: - - Molecular biology - - Genetics + resources: + - title: .nan + url: .nan - biocontainers: links + biotools: links bunya: '' description: LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. + edam-operations: + - term: Scaffolding + url: http://edamontology.org/operation_3216 + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: Read mapping + url: http://edamontology.org/operation_3198 + - term: Read pre-processing + url: http://edamontology.org/operation_3219 + - term: Sequence trimming + url: http://edamontology.org/operation_3192 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Mapping + url: http://edamontology.org/topic_0102 + - term: Sequencing + url: http://edamontology.org/topic_3168 galaxy: - description: 'LINKS: - scaffold genome assemblies with long reads' title: LINKS 2.0.1+galaxy+1 @@ -9238,20 +11281,25 @@ - title: 'LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads' url: https://doi.org/10.1186/s13742-015-0076-3 - registry-link: links - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - Mapping - - Sequencing + resources: + - title: .nan + url: .nan - biocontainers: lofreq + biotools: lofreq bunya: '' description: LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering. + edam-operations: + - term: Variant calling + url: http://edamontology.org/operation_3227 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Genetic variation + url: http://edamontology.org/topic_0199 galaxy: - description: 'Add LoFreq alignment quality scores: to aligned read SAM/BAM records' title: Add LoFreq alignment quality scores 2.1.5+galaxy1 @@ -9279,13 +11327,11 @@ - title: 'LoFreq: A sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets' url: https://doi.org/10.1093/nar/gks918 - registry-link: lofreq - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Genetic variation + resources: + - title: .nan + url: .nan - biocontainers: longshot + biotools: longshot bunya: '' description: Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies @@ -9294,6 +11340,12 @@ It can output haplotype-separated BAM files that can be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs), but it can genotype indels if they are given in an input VCF. + edam-operations: + - term: Variant calling + url: http://edamontology.org/operation_3227 + edam-topics: + - term: Genetic variation + url: http://edamontology.org/topic_0199 galaxy: '' homepage: https://github.com/pjedge/longshot id: longshot @@ -9307,16 +11359,17 @@ - title: Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing url: https://doi.org/10.1038/s41467-019-12493-y - registry-link: longshot - resource-description: .nan - resource-documentation: .nan - topics: - - Genetic variation + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 5.5.2.11-gcc-10.3.0 - 5.5.2.11-gcc-11.3.0 (D) description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: http://lpsolve.sourceforge.net/5.5/ id: lpsolve @@ -9327,15 +11380,21 @@ - 5.5.2.11 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: ltr_retriever + biotools: ltr_retriever bunya: '' description: LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package. + edam-operations: + - term: Sequence assembly + url: http://edamontology.org/operation_0310 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: '' homepage: https://github.com/oushujun/LTR_retriever id: ltr_retriever @@ -9349,16 +11408,17 @@ - title: 'LTR_retriever: A highly accurate and sensitive program for identification of long terminal repeat retrotransposons' url: https://doi.org/10.1104/pp.17.01310 - registry-link: ltr_retriever - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 5.4.3-gcccore-10.3.0 - 5.4.4-gcccore-11.3.0 (D) description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://www.lua.org/ id: lua @@ -9368,14 +11428,28 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: macs + biotools: macs bunya: - 2.2.9.1 description: Model-based Analysis of ChIP-seq data. + edam-operations: + - term: Peak calling + url: http://edamontology.org/operation_3222 + - term: Enrichment analysis + url: http://edamontology.org/operation_3501 + - term: Gene regulatory network analysis + url: http://edamontology.org/operation_1781 + edam-topics: + - term: ChIP-seq + url: http://edamontology.org/topic_3169 + - term: Molecular interactions, pathways and networks + url: http://edamontology.org/topic_0602 + - term: Transcription factors and regulatory sites + url: http://edamontology.org/topic_0749 galaxy: - description: 'MACS2 bdgdiff: Differential peak detection based on paired four bedgraph files' @@ -9420,18 +11494,17 @@ publications: - title: Model-based analysis of ChIP-Seq (MACS) url: http://www.ncbi.nlm.nih.gov/pubmed/18798982 - registry-link: macs - resource-description: .nan - resource-documentation: .nan - topics: - - ChIP-seq - - Molecular interactions, pathways and networks - - Transcription factors and regulatory sites + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 1.3.0-gompi-2021a - 1.3.0-gompi-2022a (D) description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: maeparser @@ -9441,13 +11514,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Extract MAF by block number: given a set of block numbers and a MAF file' @@ -9461,13 +11536,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Filter MAF: by specified attributes' title: Filter MAF 1.0.1 @@ -9480,13 +11557,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Filter MAF blocks: by Size' title: Filter MAF blocks 1.0.1 @@ -9499,13 +11578,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Filter MAF blocks: by Species' title: Filter MAF blocks 1.0.0 @@ -9518,13 +11599,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Reverse Complement: a MAF file' title: Reverse Complement 1.0.1 @@ -9537,13 +11620,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Split MAF blocks: by Species' title: Split MAF blocks 1.0.0 @@ -9556,13 +11641,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'MAF Coverage Stats: Alignment coverage information' title: MAF Coverage Stats 1.0.1 @@ -9575,13 +11662,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Join MAF blocks: by Species' title: Join MAF blocks 1.0.0 @@ -9594,13 +11683,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'MAF to BED: Converts a MAF formatted file to the BED format' title: MAF to BED 1.0.0 @@ -9613,13 +11704,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'MAF to FASTA: Converts a MAF formatted file to FASTA format' title: MAF to FASTA 1.0.1 @@ -9632,13 +11725,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'MAF to Interval: Converts a MAF formatted file to the Interval format' title: MAF to Interval 1.0.0 @@ -9651,15 +11746,21 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: MAFFT + biotools: MAFFT bunya: - 7.490-gcc-10.3.0-with-extensions description: MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. + edam-operations: + - term: Multiple sequence alignment + url: http://edamontology.org/operation_0492 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'MAFFT: Multiple alignment program for amino acid or nucleotide sequences' title: MAFFT 7.520+galaxy0 @@ -9675,6 +11776,7 @@ nci-gadi: '' nci-if89: - '7.505' + - '7.525' pawsey: '' publications: - title: 'MAFFT: Iterative refinement and additional methods' @@ -9691,15 +11793,24 @@ url: https://doi.org/10.1093/molbev/mst010 - title: 'MAFFT version 5: Improvement in accuracy of multiple sequence alignment' url: https://doi.org/10.1093/nar/gki198 - registry-link: MAFFT - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: mageck + biotools: mageck bunya: '' description: Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. + edam-operations: + - term: Genetic variation analysis + url: http://edamontology.org/operation_3197 + edam-topics: + - term: Genetics + url: http://edamontology.org/topic_3053 + - term: Genetic variation + url: http://edamontology.org/topic_0199 + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: - description: 'MAGeCK count: - collect sgRNA read counts from read mapping files' title: MAGeCK count 0.5.9.2.4 @@ -9729,19 +11840,26 @@ publications: - title: Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR url: http://www.ncbi.nlm.nih.gov/pubmed/26673418 - registry-link: mageck - resource-description: .nan - resource-documentation: .nan - topics: - - Genetics - - Genetic variation - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: maker + biotools: maker bunya: - 3.01.03--pl5262h8f1cd36_2 description: "Portable and easily configurable genome annotation pipeline. It\u2019\ s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently\ \ annotate their genomes and to create genome databases." + edam-operations: + - term: Genome annotation + url: http://edamontology.org/operation_0362 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: DNA + url: http://edamontology.org/topic_0654 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'Maker: genome annotation pipeline' title: Maker 2.31.11+galaxy2 @@ -9763,14 +11881,11 @@ url: https://doi.org/10.1101/gr.6743907 - title: 10.1186/1471-2105-12-491 url: https://doi.org/10.1186/1471-2105-12-491 - registry-link: maker - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - DNA - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: maldi_quant + biotools: maldi_quant bunya: '' description: MALDIquant is a complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass @@ -9779,6 +11894,22 @@ morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions. + edam-operations: + - term: Quantification + url: http://edamontology.org/operation_3799 + - term: Visualisation + url: http://edamontology.org/operation_0337 + - term: Spectrum calculation + url: http://edamontology.org/operation_3860 + - term: Peak detection + url: http://edamontology.org/operation_3215 + - term: Mass spectra calibration + url: http://edamontology.org/operation_3627 + edam-topics: + - term: Proteomics experiment + url: http://edamontology.org/topic_3520 + - term: Proteomics + url: http://edamontology.org/topic_0121 galaxy: - description: 'MALDIquant peak detection: Peak detection, binning and filtering for mass-spectrometry imaging data' @@ -9799,16 +11930,28 @@ - title: 'Maldiquant: A versatile R package for the analysis of mass spectrometry data' url: https://doi.org/10.1093/bioinformatics/bts447 - registry-link: maldi_quant - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics experiment - - Proteomics + resources: + - title: .nan + url: .nan - biocontainers: mash + biotools: mash bunya: - 2.3-gcc-10.3.0 description: Fast genome and metagenome distance estimation using MinHash. + edam-operations: + - term: Sequence distance matrix generation + url: http://edamontology.org/operation_0289 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Statistics and probability + url: http://edamontology.org/topic_2269 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: DNA mutation + url: http://edamontology.org/topic_2533 galaxy: '' homepage: https://github.com/marbl/mash id: mash @@ -9820,18 +11963,15 @@ publications: - title: 10.1186/s13059-016-0997-x url: https://doi.org/10.1186/s13059-016-0997-x - registry-link: mash - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Metagenomics - - Statistics and probability - - Sequence analysis - - DNA mutation + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'mash screen: determines how well query sequences are contained within a pool of sequences' @@ -9845,13 +11985,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'mash sketch: Create a reduced representation of a sequence or set of sequences, based on min-hashes' @@ -9865,13 +12007,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'MasterVar to pgSnp: Convert from MasterVar to pgSnp format' title: MasterVar to pgSnp 1.0.0 @@ -9884,16 +12028,26 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: masurca + biotools: masurca bunya: '' description: "Whole genome assembly software. It combines the efficiency of the\ \ de\_Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can\ \ assemble data sets containing only short reads from Illumina sequencing or a\ \ mixture of short reads and long reads (Sanger, 454)." + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Whole genome sequencing + url: http://edamontology.org/topic_3673 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'MaSuRCA simple: The MaSuRCA (Maryland Super Read Cabog Assembler) genome assembly and analysis toolkit without config' @@ -9909,16 +12063,23 @@ publications: - title: The MaSuRCA genome assembler url: http://www.ncbi.nlm.nih.gov/pubmed/23990416 - registry-link: masurca - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - Whole genome sequencing - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: matchms + biotools: matchms bunya: '' description: Tool to import, process, clean, and compare mass spectrometry data. + edam-operations: + - term: Spectral library search + url: http://edamontology.org/operation_3801 + - term: Format validation + url: http://edamontology.org/operation_0336 + - term: Filtering + url: http://edamontology.org/operation_3695 + edam-topics: + - term: Metabolomics + url: http://edamontology.org/topic_3172 galaxy: - description: 'matchms convert: convert between mass spectral library formats (.mgf/.msp/.json) using matchms' @@ -9968,18 +12129,23 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: matchms - resource-description: .nan - resource-documentation: .nan - topics: - - Metabolomics + resources: + - title: .nan + url: .nan - biocontainers: matplotlib + biotools: matplotlib bunya: - 3.4.2-foss-2021a - 3.5.2-foss-2022a (D) description: Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python. Matplotlib makes easy things easy and hard things possible. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + - term: Visualisation + url: http://edamontology.org/operation_0337 + edam-topics: '' galaxy: '' homepage: https://matplotlib.org/ id: matplotlib @@ -9989,14 +12155,24 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: matplotlib - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: maxbin + biotools: maxbin bunya: '' description: Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. + edam-operations: + - term: Sequence assembly + url: http://edamontology.org/operation_0310 + edam-topics: + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Microbiology + url: http://edamontology.org/topic_3301 galaxy: - description: 'MaxBin2: clusters metagenomic contigs into bins' title: MaxBin2 2.2.7+galaxy2 @@ -10011,18 +12187,39 @@ publications: - title: '26515820' url: http://www.ncbi.nlm.nih.gov/pubmed/26515820 - registry-link: maxbin - resource-description: .nan - resource-documentation: .nan - topics: - - Metagenomics - - Sequence assembly - - Microbiology + resources: + - title: .nan + url: .nan - biocontainers: maxquant + biotools: maxquant bunya: - 2.2.0.0-gcccore-11.3.0 description: Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. + edam-operations: + - term: Imputation + url: http://edamontology.org/operation_3557 + - term: Visualisation + url: http://edamontology.org/operation_0337 + - term: Protein quantification + url: http://edamontology.org/operation_3630 + - term: Statistical calculation + url: http://edamontology.org/operation_2238 + - term: Standardisation and normalisation + url: http://edamontology.org/operation_3435 + - term: Heat map generation + url: http://edamontology.org/operation_0531 + - term: Clustering + url: http://edamontology.org/operation_3432 + - term: Principal component plotting + url: http://edamontology.org/operation_2939 + edam-topics: + - term: Proteomics experiment + url: http://edamontology.org/topic_3520 + - term: Proteomics + url: http://edamontology.org/topic_0121 + - term: Statistics and probability + url: http://edamontology.org/topic_2269 galaxy: - description: 'MaxQuant (using mqpar.xml): ' title: MaxQuant (using mqpar.xml) 2.0.3.0+galaxy0 @@ -10051,17 +12248,24 @@ - title: MaxQuant.Live Enables Enhanced Selectivity and Identification of Peptides Modified by Endogenous SUMO and Ubiquitin url: https://doi.org/10.1021/ACS.JPROTEOME.0C00892 - registry-link: maxquant - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics experiment - - Proteomics - - Statistics and probability + resources: + - title: .nan + url: .nan - biocontainers: mcl + biotools: mcl bunya: '' description: MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. + edam-operations: + - term: Clustering + url: http://edamontology.org/operation_3432 + - term: Network analysis + url: http://edamontology.org/operation_3927 + - term: Gene regulatory network analysis + url: http://edamontology.org/operation_1781 + edam-topics: + - term: Molecular interactions, pathways and networks + url: http://edamontology.org/topic_0602 galaxy: '' homepage: http://micans.org/mcl/ id: mcl @@ -10074,18 +12278,23 @@ publications: - title: 10.1007/978-1-61779-361-5_15 url: https://doi.org/10.1007/978-1-61779-361-5_15 - registry-link: mcl - resource-description: .nan - resource-documentation: .nan - topics: - - Molecular interactions, pathways and networks + resources: + - title: .nan + url: .nan - biocontainers: mdanalysis + biotools: mdanalysis bunya: '' description: MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, Amber or DL_POLY; it also reads other formats (e.g. PDB files and XYZ format trajectories; see the supported coordinate formats for the full list). It can write most of these formats, too, together with atom selections for use in Gromacs, CHARMM, VMD and PyMol + edam-operations: + - term: Molecular dynamics + url: http://edamontology.org/operation_2476 + edam-topics: + - term: Molecular dynamics + url: http://edamontology.org/topic_0176 galaxy: - description: 'Cosine Content: - measure the cosine content of the PCA projection' title: Cosine Content 1.0.0+galaxy0 @@ -10100,14 +12309,15 @@ publications: - title: 'MDAnalysis: A toolkit for the analysis of molecular dynamics simulations' url: https://doi.org/10.1002/jcc.21787 - registry-link: mdanalysis - resource-description: .nan - resource-documentation: .nan - topics: - - Molecular dynamics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Slice MD trajectories: using the MDTraj package' title: Slice MD trajectories 1.9.7+galaxy0 @@ -10124,16 +12334,28 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: medaka + biotools: medaka bunya: - 1.9.1 description: medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. + edam-operations: + - term: Base-calling + url: http://edamontology.org/operation_3185 + - term: Variant calling + url: http://edamontology.org/operation_3227 + - term: Sequence assembly + url: http://edamontology.org/operation_0310 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Machine learning + url: http://edamontology.org/topic_3474 galaxy: - description: 'medaka variant pipeline: via neural networks' title: medaka variant pipeline 1.4.4+galaxy1 @@ -10156,19 +12378,29 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: medaka - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - Machine learning + resources: + - title: .nan + url: .nan - biocontainers: megahit + biotools: megahit bunya: - 1.2.9-gcccore-10.3.0 - 1.2.9-gcccore-11.3.0 (D) description: Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + edam-topics: + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Ecology + url: http://edamontology.org/topic_0610 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: - description: 'MEGAHIT: for metagenomics assembly' title: MEGAHIT 1.2.9+galaxy1 @@ -10184,17 +12416,15 @@ - title: 'MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph' url: http://www.ncbi.nlm.nih.gov/pubmed/25609793 - registry-link: megahit - resource-description: .nan - resource-documentation: .nan - topics: - - Metagenomics - - Sequencing - - Ecology - - Sequence assembly + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Merge Columns: together' title: Merge Columns 1.0.3 @@ -10207,11 +12437,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: merqury + biotools: merqury bunya: '' description: 'Reference-free quality, completeness, and phasing assessment for genome assemblies. @@ -10224,35 +12454,63 @@ Merqury provides a set of tools for this purpose.' + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: k-mer counting + url: http://edamontology.org/operation_3472 + - term: Scaffolding + url: http://edamontology.org/operation_3216 + - term: Phasing + url: http://edamontology.org/operation_3454 + - term: De-novo assembly + url: http://edamontology.org/operation_0524 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Whole genome sequencing + url: http://edamontology.org/topic_3673 + - term: Plant biology + url: http://edamontology.org/topic_0780 galaxy: - description: 'Merqury: evaluate the assembly quality' - title: Merqury 1.3+galaxy3 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmerqury%2Fmerqury%2F1.3%2Bgalaxy3 + title: Merqury 1.3+galaxy4 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmerqury%2Fmerqury%2F1.3%2Bgalaxy4 - description: 'Merqury histogram plot: evaluate the assembly quality' - title: Merqury histogram plot 1.3+galaxy3 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmerqury%2Fmerquryplot%2F1.3%2Bgalaxy3 + title: Merqury histogram plot 1.3+galaxy4 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmerqury%2Fmerquryplot%2F1.3%2Bgalaxy4 homepage: https://github.com/marbl/merqury id: merqury license: '' name: Merqury nci-gadi: '' - nci-if89: '' + nci-if89: + - '1.3' pawsey: '' publications: - title: 10.1101/2020.03.15.992941 url: https://doi.org/10.1101/2020.03.15.992941 - registry-link: merqury - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - Whole genome sequencing - - Plant biology + resources: + - title: .nan + url: .nan - biocontainers: meryl + biotools: meryl bunya: '' description: Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. + edam-operations: + - term: k-mer counting + url: http://edamontology.org/operation_3472 + edam-topics: + - term: Whole genome sequencing + url: http://edamontology.org/topic_3673 + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Sequencing + url: http://edamontology.org/topic_3168 galaxy: - description: 'Meryl: a genomic k-mer counter and sequence utility' title: Meryl 1.3+galaxy6 @@ -10262,26 +12520,37 @@ license: Freeware name: meryl nci-gadi: '' - nci-if89: '' + nci-if89: + - 1.4.1 pawsey: '' publications: - title: 10.1186/s13059-020-02134-9 url: https://doi.org/10.1186/s13059-020-02134-9 - registry-link: meryl - resource-description: .nan - resource-documentation: .nan - topics: - - Whole genome sequencing - - Genomics - - Sequence analysis - - Sequencing + resources: + - title: .nan + url: .nan - biocontainers: MetaBAT_2 + biotools: MetaBAT_2 bunya: '' description: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different "bins", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning + edam-operations: + - term: Read binning + url: http://edamontology.org/operation_3798 + - term: Sequence assembly + url: http://edamontology.org/operation_0310 + - term: Genome annotation + url: http://edamontology.org/operation_0362 + edam-topics: + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Metagenomic sequencing + url: http://edamontology.org/topic_3837 galaxy: - description: 'MetaBAT2: metagenome binning' title: MetaBAT2 2.15+galaxy3 @@ -10300,16 +12569,15 @@ - title: MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities url: https://doi.org/10.7717/peerj.1165 - registry-link: MetaBAT_2 - resource-description: .nan - resource-documentation: .nan - topics: - - Metagenomics - - Sequence assembly - - Metagenomic sequencing + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'metabolicMine: server' title: metabolicMine 1.0.0 @@ -10322,11 +12590,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: MetaDEGalaxy + biotools: MetaDEGalaxy bunya: '' description: 'Galaxy workflow for differential abundance analysis of 16s metagenomic data. @@ -10338,6 +12606,24 @@ This history is empty. You can load your own data or get data from an external source' + edam-operations: + - term: Read pre-processing + url: http://edamontology.org/operation_3219 + - term: Standardisation and normalisation + url: http://edamontology.org/operation_3435 + - term: Sequence merging + url: http://edamontology.org/operation_0232 + edam-topics: + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Metagenomic sequencing + url: http://edamontology.org/topic_3837 + - term: Workflows + url: http://edamontology.org/topic_0769 + - term: Microbial ecology + url: http://edamontology.org/topic_3697 + - term: RNA-Seq + url: http://edamontology.org/topic_3170 galaxy: - description: 'PEAR Statistics: Generate paired-end reads overlap Statistic from PEAR log file' @@ -10381,21 +12667,24 @@ - title: 'MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data' url: https://doi.org/10.12688/F1000RESEARCH.18866.2 - registry-link: MetaDEGalaxy - resource-description: .nan - resource-documentation: .nan - topics: - - Metagenomics - - Metagenomic sequencing - - Workflows - - Microbial ecology - - RNA-Seq + resources: + - title: .nan + url: .nan - biocontainers: MetaEuk + biotools: MetaEuk bunya: - 5-gcc-10.3.0 - 6-gcc-11.3.0 (D) description: MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics + edam-operations: + - term: Homology-based gene prediction + url: http://edamontology.org/operation_3663 + edam-topics: + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Gene and protein families + url: http://edamontology.org/topic_0623 galaxy: '' homepage: https://metaeuk.soedinglab.org/ id: metaeuk @@ -10410,23 +12699,31 @@ url: https://doi.org/10.1186/s40168-020-00808-x - title: 10.1101/851964 url: https://doi.org/10.1101/851964 - registry-link: MetaEuk - resource-description: .nan - resource-documentation: .nan - topics: - - Metagenomics - - Gene and protein families + resources: + - title: .nan + url: .nan - biocontainers: metaphlan + biotools: metaphlan bunya: '' description: Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. + edam-operations: + - term: Nucleic acid sequence analysis + url: http://edamontology.org/operation_2478 + - term: Phylogenetic tree analysis + url: http://edamontology.org/operation_0324 + edam-topics: + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Phylogenomics + url: http://edamontology.org/topic_0194 galaxy: - description: 'MetaPhlAn: to profile the composition of microbial communities' - title: MetaPhlAn 4.0.6+galaxy2 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmetaphlan%2Fmetaphlan%2F4.0.6%2Bgalaxy2 + title: MetaPhlAn 4.0.6+galaxy3 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmetaphlan%2Fmetaphlan%2F4.0.6%2Bgalaxy3 - description: 'Merge: MetaPhlAn abundance tables' - title: Merge 4.0.6+galaxy2 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmerge_metaphlan_tables%2Fmerge_metaphlan_tables%2F4.0.6%2Bgalaxy2 + title: Merge 4.0.6+galaxy3 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmerge_metaphlan_tables%2Fmerge_metaphlan_tables%2F4.0.6%2Bgalaxy3 - description: 'MetaPhlAn2: to profile the composition of microbial communities' title: MetaPhlAn2 2.6.0.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmetaphlan2%2Fmetaphlan2%2F2.6.0.1 @@ -10444,19 +12741,49 @@ - title: Metagenomic microbial community profiling using unique clade-specific marker genes url: https://doi.org/10.1038/nmeth.2066 - registry-link: metaphlan - resource-description: .nan - resource-documentation: .nan - topics: - - Metagenomics - - Phylogenomics + resources: + - title: .nan + url: .nan - biocontainers: metaQuantome + biotools: metaQuantome bunya: '' description: metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. + edam-operations: + - term: Principal component visualisation + url: http://edamontology.org/operation_2939 + - term: Visualisation + url: http://edamontology.org/operation_0337 + - term: Functional clustering + url: http://edamontology.org/operation_3459 + - term: Query and retrieval + url: http://edamontology.org/operation_0224 + - term: Differential protein expression analysis + url: http://edamontology.org/operation_3741 + - term: Heat map generation + url: http://edamontology.org/operation_0531 + - term: Quantification + url: http://edamontology.org/operation_3799 + - term: Indexing + url: http://edamontology.org/operation_0227 + - term: Filtering + url: http://edamontology.org/operation_3695 + - term: Statistical inference + url: http://edamontology.org/operation_3658 + edam-topics: + - term: Proteomics + url: http://edamontology.org/topic_0121 + - term: Metatranscriptomics + url: http://edamontology.org/topic_3941 + - term: Microbial ecology + url: http://edamontology.org/topic_3697 + - term: Proteomics experiment + url: http://edamontology.org/topic_3520 + - term: Metagenomics + url: http://edamontology.org/topic_3174 galaxy: - description: 'metaQuantome: database: download the GO, EC, and NCBI databases' title: 'metaQuantome: database 2.0.2+galaxy0' @@ -10492,22 +12819,25 @@ url: https://doi.org/10.1074/mcp.RA118.001240 - title: Updates on metaQuantome Software for Quantitative Metaproteomics url: https://doi.org/10.1021/ACS.JPROTEOME.0C00960 - registry-link: metaQuantome - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics - - Metatranscriptomics - - Microbial ecology - - Proteomics experiment - - Metagenomics + resources: + - title: .nan + url: .nan - biocontainers: metaspades + biotools: metaspades bunya: '' description: Genome assembler for metagenomics datasets. + edam-operations: + - term: Genome alignment + url: http://edamontology.org/operation_3182 + edam-topics: + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'metaSPAdes: metagenome assembler' - title: metaSPAdes 3.15.5+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fmetaspades%2Fmetaspades%2F3.15.5%2Bgalaxy1 + title: metaSPAdes 3.15.5+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fmetaspades%2Fmetaspades%2F3.15.5%2Bgalaxy2 homepage: http://cab.spbu.ru/software/spades/ id: metaspades license: '' @@ -10524,22 +12854,38 @@ url: https://doi.org/10.1093/nar/gkw343 - title: 10.7490/f1000research.1114334.1 url: https://doi.org/10.7490/f1000research.1114334.1 - registry-link: metaspades - resource-description: .nan - resource-documentation: .nan - topics: - - Metagenomics - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: metawrap + biotools: metawrap bunya: '' description: 'MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.' + edam-operations: + - term: Read binning + url: http://edamontology.org/operation_3798 + - term: Sequence assembly + url: http://edamontology.org/operation_0310 + - term: Genome annotation + url: http://edamontology.org/operation_0362 + - term: Sequence trimming + url: http://edamontology.org/operation_3192 + - term: Demultiplexing + url: http://edamontology.org/operation_3933 + edam-topics: + - term: Whole genome sequencing + url: http://edamontology.org/topic_3673 + - term: Metagenomic sequencing + url: http://edamontology.org/topic_3837 + - term: Metagenomics + url: http://edamontology.org/topic_3174 galaxy: - description: 'MetaWRAP: metagenome binning pipeline' - title: MetaWRAP 1.3.0+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxy-australia%2Fmetawrapmg_binning%2Fmetawrapmg_binning%2F1.3.0%2Bgalaxy0 + title: MetaWRAP 1.3.0+galaxy1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgalaxy-australia%2Fmetawrapmg_binning%2Fmetawrapmg_binning%2F1.3.0%2Bgalaxy1 homepage: https://github.com/bxlab/metaWRAP id: metawrap license: MIT @@ -10552,16 +12898,21 @@ 08 Information and Computing Sciences 0803 Computer Software 08 Information and Computing Sciences 0806 Information Systems url: https://doi.org/10.1186/s40168-018-0541-1 - registry-link: metawrap - resource-description: .nan - resource-documentation: .nan - topics: - - Whole genome sequencing - - Metagenomic sequencing - - Metagenomics + resources: + - title: .nan + url: .nan - biocontainers: methyldackel + biotools: methyldackel bunya: '' description: A (mostly) universal methylation extractor for BS-seq experiments. + edam-operations: + - term: Sequence alignment conversion + url: http://edamontology.org/operation_0260 + - term: Methylation calling + url: http://edamontology.org/operation_3919 + edam-topics: + - term: Epigenomics + url: http://edamontology.org/topic_3173 galaxy: - description: 'MethylDackel: A tool for processing bisulfite sequencing alignments' title: MethylDackel 0.5.2+galaxy0 @@ -10574,14 +12925,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: methyldackel - resource-description: .nan - resource-documentation: .nan - topics: - - Epigenomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'metilene: calling differentially methylated regions from bisulfite sequencing data' @@ -10595,15 +12947,29 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: MIGRATE + biotools: MIGRATE bunya: '' description: Estimates effective population sizes,past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes, and population divergences or admixture. + edam-operations: + - term: Haplotype mapping + url: http://edamontology.org/operation_0487 + - term: Phylogenetic tree generation (maximum likelihood and Bayesian methods) + url: http://edamontology.org/operation_0547 + - term: Cell migration analysis + url: http://edamontology.org/operation_3446 + edam-topics: + - term: Population genetics + url: http://edamontology.org/topic_3056 + - term: Nucleic acid structure analysis + url: http://edamontology.org/topic_0097 + - term: Zoology + url: http://edamontology.org/topic_3500 galaxy: '' homepage: https://peterbeerli.com/migrate-html5/index.html id: MIGRATE @@ -10618,18 +12984,27 @@ url: https://doi.org/10.1534/genetics.109.112532 - title: Fractional coalescent url: https://doi.org/10.1073/pnas.1810239116 - registry-link: MIGRATE - resource-description: Install and testing on Gadi (NCI) - resource-documentation: https://github.com/AustralianBioCommons/migrate - topics: - - Population genetics - - Nucleic acid structure analysis - - Zoology + resources: + - title: Install and testing on Gadi (NCI) + url: https://github.com/AustralianBioCommons/migrate - biocontainers: mikado + biotools: mikado bunya: - 2.2.4--py39h70b41aa_0 description: A lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data and to select the best models in each locus. + edam-operations: + - term: Splice transcript prediction + url: http://edamontology.org/operation_0264 + - term: Gene prediction + url: http://edamontology.org/operation_2454 + - term: RNA-Seq analysis + url: http://edamontology.org/operation_3680 + edam-topics: + - term: RNA-seq + url: http://edamontology.org/topic_3170 + - term: Gene transcripts + url: http://edamontology.org/topic_3512 galaxy: '' homepage: https://github.com/lucventurini/mikado id: mikado @@ -10642,15 +13017,15 @@ - title: Leveraging multiple transcriptome assembly methods for improved gene structure annotation url: https://doi.org/10.1093/gigascience/giy093 - registry-link: mikado - resource-description: .nan - resource-documentation: .nan - topics: - - RNA-seq - - Gene transcripts + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'MiModD Read Alignment: maps sequence reads to a reference genome using SNAP' @@ -10716,14 +13091,20 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: minia + biotools: minia bunya: '' description: Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: - description: 'Minia: Short-read assembler based on a de Bruijn graph' title: Minia 3.2.6 @@ -10739,16 +13120,23 @@ - title: Using cascading Bloom filters to improve the memory usage for de Brujin graphs url: https://doi.org/10.1186/1748-7188-9-2 - registry-link: minia - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly + resources: + - title: .nan + url: .nan - biocontainers: miniasm + biotools: miniasm bunya: '' description: Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. + edam-operations: + - term: De-novo assembly + url: http://edamontology.org/operation_0524 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: - description: 'miniasm: Ultrafast de novo assembly for long noisy reads' title: miniasm 0.3_r179+galaxy1 @@ -10765,16 +13153,16 @@ - title: 'Minimap and miniasm: Fast mapping and de novo assembly for noisy long sequences' url: https://doi.org/10.1093/bioinformatics/btw152 - registry-link: miniasm - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Sequence assembly + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 4.12.0 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://docs.conda.io/en/latest/miniconda.html id: miniconda @@ -10785,14 +13173,20 @@ - 4.12.0 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: minimap2 + biotools: minimap2 bunya: - 2.24-gcccore-11.3.0 description: Pairwise aligner for genomic and spliced nucleotide sequences + edam-operations: + - term: Pairwise sequence alignment + url: http://edamontology.org/operation_0491 + edam-topics: + - term: Mapping + url: http://edamontology.org/topic_0102 galaxy: - description: 'Map with minimap2: A fast pairwise aligner for genomic and spliced nucleotide sequences' @@ -10806,21 +13200,31 @@ - '2.17' - '2.22' - '2.24' - nci-if89: '' + nci-if89: + - '2.26' pawsey: '' publications: - title: 'Minimap2: Pairwise alignment for nucleotide sequences' url: https://doi.org/10.1093/bioinformatics/bty191 - registry-link: minimap2 - resource-description: .nan - resource-documentation: .nan - topics: - - Mapping + resources: + - title: .nan + url: .nan - biocontainers: miniprot + biotools: miniprot bunya: '' description: Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. + edam-operations: + - term: Sequence alignment + url: http://edamontology.org/operation_0292 + - term: Protein sequence analysis + url: http://edamontology.org/operation_2479 + edam-topics: + - term: Sequence sites, features and motifs + url: http://edamontology.org/topic_0160 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: '' homepage: https://github.com/lh3/miniprot id: miniprot @@ -10831,16 +13235,28 @@ - '0.5' pawsey: '' publications: '' - registry-link: miniprot - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence sites, features and motifs - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: mira + biotools: mira bunya: - 4.9.6--1 description: MIRA 3 - Whole Genome Shotgun and EST Sequence Assembler + edam-operations: + - term: Local alignment + url: http://edamontology.org/operation_0495 + - term: k-mer counting + url: http://edamontology.org/operation_3472 + - term: Sequence assembly + url: http://edamontology.org/operation_0310 + - term: Read mapping + url: http://edamontology.org/operation_3198 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: RNA-Seq + url: http://edamontology.org/topic_3170 galaxy: '' homepage: https://sourceforge.net/p/mira-assembler/wiki/Home/ id: mira @@ -10853,15 +13269,15 @@ - title: Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs url: http://www.ncbi.nlm.nih.gov/pubmed/15140833 - registry-link: mira - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - RNA-Seq + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'miRcounts: Counts miRNA alignments from small RNA sequence data' title: miRcounts 1.4.0 @@ -10874,14 +13290,24 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: mirdeep2 + biotools: mirdeep2 bunya: '' description: miRDeep2 discovers active known or novel miRNAs from deep sequencing data. + edam-operations: + - term: miRNA target prediction + url: http://edamontology.org/operation_0463 + - term: miRNA expression analysis + url: http://edamontology.org/operation_3792 + edam-topics: + - term: Functional, regulatory and non-coding RNA + url: http://edamontology.org/topic_0659 + - term: RNA immunoprecipitation + url: http://edamontology.org/topic_3794 galaxy: - description: 'MiRDeep2: identification of novel and known miRNAs' title: MiRDeep2 2.0.1.2+galaxy0 @@ -10901,15 +13327,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: mirdeep2 - resource-description: .nan - resource-documentation: .nan - topics: - - Functional, regulatory and non-coding RNA - - RNA immunoprecipitation + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'MITObim: mitochondrial baiting and iterative mapping' title: MITObim 1.9.1 @@ -10922,13 +13348,29 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: mitohifi + biotools: mitohifi bunya: '' description: Find, circularise and annotate mitogenome from PacBio assemblies + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: De-novo assembly + url: http://edamontology.org/operation_0524 + - term: Genome annotation + url: http://edamontology.org/operation_0362 + - term: Sequence classification + url: http://edamontology.org/operation_2995 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: - description: 'MitoHiFi: assembly mitogenomes from Pacbio HiFi reads' title: MitoHiFi 3+galaxy0 @@ -10944,20 +13386,25 @@ - title: 'MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics' url: https://doi.org/10.1111/1755-0998.13160 - registry-link: mitohifi - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - Sequence analysis - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: mitos + biotools: mitos bunya: '' description: De novo metazoan mitochondrial genome annotation. + edam-operations: + - term: Genome annotation + url: http://edamontology.org/operation_0362 + edam-topics: + - term: Zoology + url: http://edamontology.org/topic_3500 + - term: Whole genome sequencing + url: http://edamontology.org/topic_3673 galaxy: - description: 'MITOS2: de-novo annotation of metazoan mitochondrial genomes' - title: MITOS2 2.1.7+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmitos2%2Fmitos2%2F2.1.7%2Bgalaxy1 + title: MITOS2 2.1.9+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmitos2%2Fmitos2%2F2.1.9%2Bgalaxy0 homepage: https://mitos.bioinf.uni-leipzig.de/index.py id: mitos2 license: '' @@ -10968,17 +13415,21 @@ publications: - title: 10.1016/j.ympev.2012.08.023 url: https://doi.org/10.1016/j.ympev.2012.08.023 - registry-link: mitos - resource-description: .nan - resource-documentation: .nan - topics: - - Zoology - - Whole genome sequencing + resources: + - title: .nan + url: .nan - biocontainers: mlst + biotools: mlst bunya: - 2.23.0--hdfd78af_1 description: Multi Locus Sequence Typing from an assembled genome or from a set of reads. + edam-operations: + - term: Multilocus sequence typing + url: http://edamontology.org/operation_3840 + edam-topics: + - term: Immunoproteins and antigens + url: http://edamontology.org/topic_2830 galaxy: - description: 'MLST: Scans genomes against PubMLST schemes' title: MLST 2.22.0 @@ -10996,12 +13447,11 @@ publications: - title: Multilocus sequence typing of total-genome-sequenced bacteria url: https://doi.org/10.1128/JCM.06094-11 - registry-link: mlst - resource-description: .nan - resource-documentation: .nan - topics: - - Immunoproteins and antigens + resources: + - title: .nan + url: .nan - biocontainers: MMseqs2 + biotools: MMseqs2 bunya: '' description: "MMseqs2 (Many-against-Many sequence searching) is a software suite\ \ to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is\ @@ -11014,6 +13464,24 @@ \ algorithm whose runtime scales linearly With Linclust we clustered 1.6 billion\ \ metagenomic sequence fragments in 10\u2009h on a single server to 50% sequence\ \ identity." + edam-operations: + - term: Sequence similarity search + url: http://edamontology.org/operation_0346 + - term: Sequence alignment + url: http://edamontology.org/operation_0292 + edam-topics: + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Proteins + url: http://edamontology.org/topic_0078 + - term: Nucleic acids + url: http://edamontology.org/topic_0077 + - term: Gene and protein families + url: http://edamontology.org/topic_0623 + - term: Taxonomy + url: http://edamontology.org/topic_0637 galaxy: '' homepage: https://mmseqs.com id: mmseqs2 @@ -11038,17 +13506,11 @@ url: https://doi.org/10.1101/2020.11.27.401018 - title: 10.1093/bioinformatics/btab184 url: https://doi.org/10.1093/bioinformatics/btab184 - registry-link: MMseqs2 - resource-description: .nan - resource-documentation: .nan - topics: - - Metagenomics - - Sequence analysis - - Proteins - - Nucleic acids - - Gene and protein families - - Taxonomy + resources: + - title: .nan + url: .nan - biocontainers: mob-suite + biotools: mob-suite bunya: '' description: 'Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance. @@ -11062,6 +13524,26 @@ adaption of bacteria to new niches through horizontal transmission of novel traits to different genetic backgrounds. The MOB-suite is designed to be a modular set of tools for the typing and reconstruction of plasmid sequences from WGS assemblies.' + edam-operations: + - term: Clustering + url: http://edamontology.org/operation_3432 + - term: Plasmid map drawing + url: http://edamontology.org/operation_0578 + - term: Sequence assembly + url: http://edamontology.org/operation_0310 + - term: Deposition + url: http://edamontology.org/operation_3431 + edam-topics: + - term: Mobile genetic elements + url: http://edamontology.org/topic_0798 + - term: Whole genome sequencing + url: http://edamontology.org/topic_3673 + - term: Public health and epidemiology + url: http://edamontology.org/topic_3305 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Biomarkers + url: http://edamontology.org/topic_3360 galaxy: - description: 'MOB-Recon: Type contigs and extract plasmid sequences' title: MOB-Recon 3.0.3+galaxy0 @@ -11080,18 +13562,15 @@ - title: Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance url: https://doi.org/10.1099/MGEN.0.000435 - registry-link: mob-suite - resource-description: .nan - resource-documentation: .nan - topics: - - Mobile genetic elements - - Whole genome sequencing - - Public health and epidemiology - - Sequence assembly - - Biomarkers + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'modENCODE fly: server' title: modENCODE fly 1.0.1 @@ -11104,13 +13583,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'modENCODE worm: server' title: modENCODE worm 1.0.1 @@ -11123,13 +13604,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'modENCODE modMine: server' title: modENCODE modMine 1.0.0 @@ -11142,13 +13625,19 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: moff + biotools: moff bunya: '' description: A modest Feature Finder to extract features in MS1 Data. + edam-operations: + - term: Protein feature detection + url: http://edamontology.org/operation_3092 + edam-topics: + - term: Proteomics + url: http://edamontology.org/topic_0121 galaxy: - description: 'moFF: extracts MS1 intensities from spectrum files' title: moFF 2.0.3.0 @@ -11163,14 +13652,15 @@ publications: - title: 'MoFF: A robust and automated approach to extract peptide ion intensities' url: https://doi.org/10.1038/nmeth.4075 - registry-link: moff - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: monailabel @@ -11180,16 +13670,23 @@ nci-if89: - 0.6.0 - 0.7.0 + - 0.8.0 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: morpheus + biotools: morpheus bunya: '' description: A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. + edam-operations: + - term: Peptide database search + url: http://edamontology.org/operation_3646 + edam-topics: + - term: Proteomics + url: http://edamontology.org/topic_0121 galaxy: - description: 'Morpheus: database search algorithm for high-resolution tandem mass spectra' @@ -11206,15 +13703,38 @@ - title: A proteomics search algorithm specifically designed for high-resolution tandem mass spectra url: https://doi.org/10.1021/pr301024c - registry-link: morpheus - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics + resources: + - title: .nan + url: .nan - biocontainers: mothur + biotools: mothur bunya: '' description: Open-source, platform-independent, community-supported software for describing and comparing microbial communities + edam-operations: + - term: DNA barcoding + url: http://edamontology.org/operation_3200 + - term: Sequencing quality control + url: http://edamontology.org/operation_3218 + - term: Sequence clustering + url: http://edamontology.org/operation_0291 + - term: Taxonomic classification + url: http://edamontology.org/operation_3460 + - term: Visualisation + url: http://edamontology.org/operation_0337 + - term: Sequence read processing + url: http://edamontology.org/operation_3921 + - term: Phylogenetic analysis + url: http://edamontology.org/operation_0324 + edam-topics: + - term: Microbial ecology + url: http://edamontology.org/topic_3697 + - term: Taxonomy + url: http://edamontology.org/topic_0637 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Phylogeny + url: http://edamontology.org/topic_0084 galaxy: - description: 'Align.check: Calculate the number of potentially misaligned bases' title: Align.check 1.39.5.0 @@ -11644,20 +14164,24 @@ publications: - title: 10.1128/AEM.01541-09 url: https://doi.org/10.1128/AEM.01541-09 - registry-link: mothur - resource-description: .nan - resource-documentation: .nan - topics: - - Microbial ecology - - Taxonomy - - Sequence analysis - - Phylogeny + resources: + - title: .nan + url: .nan - biocontainers: mousemine + biotools: mousemine bunya: '' description: Data warehouse for accessing mouse data from Mouse Genome Informatics (MGI). Supports powerful query, reporting, and analysis capabilities, the ability to save and combine results from different queries, easy integration into larger workflows, and a comprehensive Web Services layer. + edam-operations: + - term: Query and retrieval + url: http://edamontology.org/operation_0224 + edam-topics: + - term: Model organisms + url: http://edamontology.org/topic_0621 + - term: Genotype and phenotype + url: http://edamontology.org/topic_0625 galaxy: - description: 'MouseMine: server' title: MouseMine 1.0.0 @@ -11672,18 +14196,22 @@ publications: - title: 'MouseMine: a new data warehouse for MGI' url: https://doi.org/10.1007/s00335-015-9573-z - registry-link: mousemine - resource-description: .nan - resource-documentation: .nan - topics: - - Model organisms - - Genotype and phenotype + resources: + - title: .nan + url: .nan - biocontainers: mrbayes + biotools: mrbayes bunya: - 3.2.7a-foss-2022a description: Program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. It uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters. + edam-operations: + - term: Phylogenetic tree generation (maximum likelihood and Bayesian methods) + url: http://edamontology.org/operation_0547 + edam-topics: + - term: Phylogenetics + url: http://edamontology.org/topic_3293 galaxy: '' homepage: http://nbisweden.github.io/MrBayes/ id: mrbayes @@ -11701,12 +14229,11 @@ - title: 'Mrbayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space' url: https://doi.org/10.1093/sysbio/sys029 - registry-link: mrbayes - resource-description: .nan - resource-documentation: .nan - topics: - - Phylogenetics + resources: + - title: .nan + url: .nan - biocontainers: MRtrix3 + biotools: MRtrix3 bunya: - 3.0.3-foss-2021a description: A fast, flexible and open software framework for medical image processing @@ -11719,6 +14246,18 @@ applications. In this article, we provide a high-level overview of the features of the MRtrix3 framework and general-purpose image processing applications provided with the software + edam-operations: + - term: Image analysis + url: http://edamontology.org/operation_3443 + - term: Visualisation + url: http://edamontology.org/operation_0337 + edam-topics: + - term: MRI + url: http://edamontology.org/topic_3444 + - term: Medical imaging + url: http://edamontology.org/topic_3384 + - term: Data visualisation + url: http://edamontology.org/topic_0092 galaxy: '' homepage: https://github.com/MRtrix3/mrtrix3 id: mrtrix @@ -11731,19 +14270,26 @@ - title: 'MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation' url: https://doi.org/10.1016/J.NEUROIMAGE.2019.116137 - registry-link: MRtrix3 - resource-description: .nan - resource-documentation: .nan - topics: - - MRI - - Medical imaging - - Data visualisation + resources: + - title: .nan + url: .nan - biocontainers: msconvert + biotools: msconvert bunya: '' description: msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI. + edam-operations: + - term: Filtering + url: http://edamontology.org/operation_3695 + - term: Formatting + url: http://edamontology.org/operation_0335 + edam-topics: + - term: Proteomics + url: http://edamontology.org/topic_0121 + - term: Proteomics experiment + url: http://edamontology.org/topic_3520 galaxy: - description: 'msconvert: Convert and/or filter mass spectrometry files' title: msconvert 3.0.20287.2 @@ -11758,15 +14304,25 @@ publications: - title: A cross-platform toolkit for mass spectrometry and proteomics url: https://doi.org/10.1038/nbt.2377 - registry-link: msconvert - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics - - Proteomics experiment + resources: + - title: .nan + url: .nan - biocontainers: msmetaenhancer + biotools: msmetaenhancer bunya: '' description: Tool for mass spectra metadata annotation. + edam-operations: + - term: Annotation + url: http://edamontology.org/operation_0226 + - term: Standardisation and normalisation + url: http://edamontology.org/operation_3435 + edam-topics: + - term: Metabolomics + url: http://edamontology.org/topic_3172 + - term: Compound libraries and screening + url: http://edamontology.org/topic_3343 + - term: Data submission, annotation and curation + url: http://edamontology.org/topic_0219 galaxy: - description: 'MSMetaEnhancer: annotate MS data' title: MSMetaEnhancer 0.3.0+galaxy1 @@ -11781,16 +14337,35 @@ publications: - title: 10.21105/joss.04494 url: https://doi.org/10.21105/joss.04494 - registry-link: msmetaenhancer - resource-description: .nan - resource-documentation: .nan - topics: - - Metabolomics - - Compound libraries and screening - - Data submission, annotation and curation + resources: + - title: .nan + url: .nan - biocontainers: msstats + biotools: msstats bunya: '' description: Statistical tool for quantitative mass spectrometry-based proteomics. + edam-operations: + - term: Statistical modelling + url: http://edamontology.org/operation_3664 + - term: Data handling + url: http://edamontology.org/operation_2409 + - term: Differential protein expression analysis + url: http://edamontology.org/operation_3741 + - term: Statistical inference + url: http://edamontology.org/operation_3658 + - term: Quantification + url: http://edamontology.org/operation_3799 + - term: Standardisation and normalisation + url: http://edamontology.org/operation_3435 + edam-topics: + - term: Proteomics + url: http://edamontology.org/topic_0121 + - term: Proteomics experiment + url: http://edamontology.org/topic_3520 + - term: Statistics and probability + url: http://edamontology.org/topic_2269 + - term: Workflows + url: http://edamontology.org/topic_0769 galaxy: - description: 'MSstats: statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry' @@ -11807,17 +14382,15 @@ - title: 'MSstats: An R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments' url: http://www.ncbi.nlm.nih.gov/pubmed/24794931 - registry-link: msstats - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics - - Proteomics experiment - - Statistics and probability - - Workflows + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'MSstatsTMT: protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling' @@ -11831,14 +14404,16 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - '20230414' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: mtag @@ -11848,11 +14423,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: multiqc + biotools: multiqc bunya: - 1.11-foss-2021a - 1.14-foss-2022a (D) @@ -11860,6 +14435,20 @@ many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. + edam-operations: + - term: Validation + url: http://edamontology.org/operation_2428 + - term: Sequencing quality control + url: http://edamontology.org/operation_3218 + edam-topics: + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Bioinformatics + url: http://edamontology.org/topic_0091 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: - description: 'MultiQC: aggregate results from bioinformatics analyses into a single report' @@ -11874,22 +14463,29 @@ nci-if89: '' pawsey: '' publications: - - title: 'MultiQC: Summarize analysis results for multiple tools and samples in - a single report' + - title: 10.1093/bioinformatics/btw354 url: https://doi.org/10.1093/bioinformatics/btw354 - registry-link: multiqc - resource-description: .nan - resource-documentation: .nan - topics: - - Sequencing - - Bioinformatics - - Sequence analysis - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: mummer + biotools: mummer bunya: '' description: MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. Basically it is a ultra-fast alignment of large-scale DNA and protein sequences + edam-operations: + - term: Sequence alignment + url: http://edamontology.org/operation_0292 + - term: Read mapping + url: http://edamontology.org/operation_3198 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Mapping + url: http://edamontology.org/topic_0102 + - term: Sequencing + url: http://edamontology.org/topic_3168 galaxy: - description: 'Delta-Filter: Filters alignment (delta) file from nucmer' title: Delta-Filter 4.0.0rc1+galaxy3 @@ -11926,16 +14522,15 @@ url: https://doi.org/10.1186/gb-2004-5-2-r12 - title: Fast algorithms for large-scale genome alignment and comparison url: https://doi.org/10.1093/nar/30.11.2478 - registry-link: mummer - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Mapping - - Sequencing + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Construct Expression Set Object: Create an ExpressionSet object from tabular and textual data' @@ -11957,13 +14552,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'mz to sqlite: Extract mzIdentML and associated proteomics datasets into a SQLite DB' @@ -11977,13 +14574,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://www.nag.com/ id: nag @@ -11998,11 +14597,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: Nanocompore + biotools: Nanocompore bunya: - 1.0.4--pyhdfd78af_0 description: 'RNA modifications detection by comparative Nanopore direct RNA sequencing. @@ -12025,6 +14624,26 @@ such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro' + edam-operations: + - term: Post-translation modification site prediction + url: http://edamontology.org/operation_0417 + - term: PolyA signal detection + url: http://edamontology.org/operation_0428 + - term: Genotyping + url: http://edamontology.org/operation_3196 + - term: k-mer counting + url: http://edamontology.org/operation_3472 + edam-topics: + - term: Functional, regulatory and non-coding RNA + url: http://edamontology.org/topic_0659 + - term: RNA-Seq + url: http://edamontology.org/topic_3170 + - term: Gene transcripts + url: http://edamontology.org/topic_3512 + - term: Transcriptomics + url: http://edamontology.org/topic_3308 + - term: Transcription factors and regulatory sites + url: http://edamontology.org/topic_0749 galaxy: - description: 'SampComp: to compare Nanopolished datasets' title: SampComp 1.0.0rc3.post2+galaxy1 @@ -12039,18 +14658,15 @@ publications: - title: 10.1101/843136 url: https://doi.org/10.1101/843136 - registry-link: Nanocompore - resource-description: .nan - resource-documentation: .nan - topics: - - Functional, regulatory and non-coding RNA - - RNA-Seq - - Gene transcripts - - Transcriptomics - - Transcription factors and regulatory sites + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'NanoFilt: Filtering and trimming of long read sequencing data' title: NanoFilt 0.1.0 @@ -12063,20 +14679,28 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: nanoplot + biotools: nanoplot bunya: '' description: NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences + edam-operations: + - term: Scatter plot plotting + url: http://edamontology.org/operation_2940 + - term: Box-Whisker plot plotting + url: http://edamontology.org/operation_2943 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: - description: 'NanoPlot: Plotting suite for Oxford Nanopore sequencing data and alignments' - title: NanoPlot 1.42.0+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fnanoplot%2Fnanoplot%2F1.42.0%2Bgalaxy0 + title: NanoPlot 1.42.0+galaxy1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fnanoplot%2Fnanoplot%2F1.42.0%2Bgalaxy1 homepage: https://github.com/wdecoster/NanoPlot id: nanoplot license: GPL-3.0 @@ -12087,16 +14711,35 @@ publications: - title: 'NanoPack: Visualizing and processing long-read sequencing data' url: https://doi.org/10.1093/bioinformatics/bty149 - registry-link: nanoplot - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: nanopolish + biotools: nanopolish bunya: - 0.14.0--hb24e783_1 description: A package for detecting cytosine methylations and genetic variations from nanopore MinION sequencing data. + edam-operations: + - term: Statistical calculation + url: http://edamontology.org/operation_2238 + - term: Genetic variation analysis + url: http://edamontology.org/operation_3197 + - term: Sequence assembly + url: http://edamontology.org/operation_0310 + - term: Methylation analysis + url: http://edamontology.org/operation_3204 + - term: Mapping + url: http://edamontology.org/operation_2429 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Genetic variation + url: http://edamontology.org/topic_0199 + - term: Statistics and probability + url: http://edamontology.org/topic_2269 galaxy: - description: 'Nanopolish variants: - Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences' @@ -12123,17 +14766,15 @@ publications: - title: Detecting DNA cytosine methylation using nanopore sequencing url: https://doi.org/10.1038/nmeth.4184 - registry-link: nanopolish - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis - - Sequencing - - Genetic variation - - Statistics and probability + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: nanosv @@ -12144,13 +14785,15 @@ - 1.2.4 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Natural Product likeness calculator: - calculates the similarity of the molecule to the structure space covered by known natural products' @@ -12164,15 +14807,25 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: ncbi_datasets + biotools: ncbi_datasets bunya: '' description: NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + - term: Sequence database search + url: http://edamontology.org/operation_0338 + - term: Data retrieval + url: http://edamontology.org/operation_2422 + edam-topics: + - term: Biological databases + url: http://edamontology.org/topic_3071 galaxy: '' homepage: https://www.ncbi.nlm.nih.gov/datasets/ id: ncbi-datasets-cli @@ -12183,16 +14836,18 @@ - 14.2.2 - 14.13.0 - 14.29.1 + - 16.6.0 pawsey: '' publications: '' - registry-link: ncbi_datasets - resource-description: .nan - resource-documentation: .nan - topics: - - Biological databases + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'NCBI Accession Download: Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API' @@ -12206,15 +14861,17 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 2.10.9-gompi-2021a - 3.0.2-gompi-2022a (D) description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://github.com/ncbi/ncbi-vdb id: ncbi-vdb @@ -12224,17 +14881,21 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: nccmp + biotools: nccmp bunya: '' description: nccmp compares two NetCDF files bitwise, semantically or with a user defined tolerance (absolute or relative percentage). Parallel comparisons are done in local memory without requiring temporary files. Highly recommended for regression testing scientific models or datasets in a test-driven development environment. + edam-operations: + - term: Regression analysis + url: http://edamontology.org/operation_3659 + edam-topics: '' galaxy: '' homepage: https://gitlab.com/remikz/nccmp id: nccmp @@ -12245,13 +14906,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: nccmp - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://www.ncl.ucar.edu/index.shtml id: ncl @@ -12262,14 +14925,16 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: nco + biotools: nco bunya: '' description: The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5. + edam-operations: '' + edam-topics: '' galaxy: '' homepage: http://nco.sourceforge.net/ id: nco @@ -12282,13 +14947,17 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: nco - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: ncview + biotools: ncview bunya: '' description: Ncview is a netCDF visual browser. + edam-operations: + - term: Visualisation + url: http://edamontology.org/operation_0337 + edam-topics: '' galaxy: '' homepage: https://cirrus.ucsd.edu/ncview/ id: ncview @@ -12299,17 +14968,19 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: ncview - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: netcdf + biotools: netcdf bunya: - 4.8.0-gompi-2021a - 4.9.0-gompi-2022a (D) description: NetCDF (Network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://www.unidata.ucar.edu/software/netcdf/ id: netcdf @@ -12332,16 +15003,30 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: netcdf - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: newick_utilities + biotools: newick_utilities bunya: '' description: The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. + edam-operations: + - term: Phylogenetic tree generation + url: http://edamontology.org/operation_0323 + - term: Phylogenetic tree analysis + url: http://edamontology.org/operation_0324 + - term: Phylogenetic tree reconstruction + url: http://edamontology.org/operation_3478 + edam-topics: + - term: Phylogeny + url: http://edamontology.org/topic_0084 + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Computer science + url: http://edamontology.org/topic_3316 galaxy: - description: 'Newick Display: visualize a phylogenetic tree' title: Newick Display 1.6+galaxy1 @@ -12356,16 +15041,15 @@ publications: - title: 10.1093/bioinformatics/btq243 url: https://doi.org/10.1093/bioinformatics/btq243 - registry-link: newick_utilities - resource-description: .nan - resource-documentation: .nan - topics: - - Phylogeny - - Genomics - - Computer science + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Nextclade: Viral genome clade assignment, mutation calling, and sequence quality checks' @@ -12379,16 +15063,30 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: nextflow + biotools: nextflow bunya: - 22.10.1 description: Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages. + edam-operations: + - term: Service composition + url: http://edamontology.org/operation_3762 + - term: Service invocation + url: http://edamontology.org/operation_3763 + edam-topics: + - term: Software engineering + url: http://edamontology.org/topic_3372 + - term: Workflows + url: http://edamontology.org/topic_0769 + - term: Bioinformatics + url: http://edamontology.org/topic_0091 + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: '' homepage: https://www.nextflow.io/ id: nextflow @@ -12402,15 +15100,11 @@ publications: - title: Nextflow enables reproducible computational workflows url: https://doi.org/10.1038/nbt.3820 - registry-link: nextflow - resource-description: .nan - resource-documentation: .nan - topics: - - Software engineering - - Workflows - - Bioinformatics - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: NextPolish + biotools: NextPolish bunya: - 1.4.1--py311he4a0461_1 description: 'A fast and efficient genome polishing tool for long read assembly. @@ -12425,6 +15119,20 @@ to correct the error bases in reference genome. To correct the raw third-generation sequencing (TGS) long reads with approximately 15-10% sequencing errors, please use NextDenovo' + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: Scaffolding + url: http://edamontology.org/operation_3216 + - term: k-mer counting + url: http://edamontology.org/operation_3472 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Plant biology + url: http://edamontology.org/topic_0780 + - term: Mapping + url: http://edamontology.org/topic_0102 galaxy: '' homepage: https://github.com/Nextomics/NextPolish id: nextpolish @@ -12436,17 +15144,16 @@ publications: - title: 'NextPolish: A fast and efficient genome polishing tool for long-read assembly' url: https://doi.org/10.1093/BIOINFORMATICS/BTZ891 - registry-link: NextPolish - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - Plant biology - - Mapping + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 0.1.0--hd03093a_0 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: nextpolish2 @@ -12456,14 +15163,16 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 2.10.9-gcccore-10.3.0 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://github.com/ncbi/ngs id: ngs @@ -12473,14 +15182,30 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: ngsutils + biotools: ngsutils bunya: '' description: NGSUtils is a suite of software tools for working with next-generation sequencing datasets + edam-operations: + - term: Read pre-processing + url: http://edamontology.org/operation_3219 + - term: Sequencing quality control + url: http://edamontology.org/operation_3218 + - term: Variant calling + url: http://edamontology.org/operation_3227 + - term: Formatting + url: http://edamontology.org/operation_0335 + - term: Sequence contamination filtering + url: http://edamontology.org/operation_3187 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Transcriptomics + url: http://edamontology.org/topic_3308 galaxy: - description: 'BAM filter: Removes reads from a BAM file based on criteria' title: BAM filter 0.5.9 @@ -12496,17 +15221,19 @@ - title: 'NGSUtils: A software suite for analyzing and manipulating next-generation sequencing datasets' url: http://www.ncbi.nlm.nih.gov/pubmed/23314324 - registry-link: ngsutils - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Transcriptomics + resources: + - title: .nan + url: .nan - biocontainers: ninja + biotools: ninja bunya: - 1.10.2-gcccore-10.3.0 - 1.10.2-gcccore-11.3.0 (D) description: Nearly Infinite Neighbor Joining Application + edam-operations: '' + edam-topics: + - term: Phylogeny + url: http://edamontology.org/topic_0084 galaxy: '' homepage: https://github.com/TravisWheelerLab/NINJA id: ninja @@ -12517,14 +15244,15 @@ - 0.98-cluster_only pawsey: '' publications: '' - registry-link: ninja - resource-description: .nan - resource-documentation: .nan - topics: - - Phylogeny + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'NOVOplasty: de novo assembler for short circular genomes' title: NOVOplasty 4.3.1+galaxy0 @@ -12537,13 +15265,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: nseg @@ -12554,13 +15284,15 @@ - 1.0.1 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Naive Variant Caller (NVC): - tabulate variable sites from BAM datasets' title: Naive Variant Caller (NVC) 0.0.4 @@ -12573,15 +15305,25 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: obitools + biotools: obitools bunya: '' description: Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. + edam-operations: + - term: Sequence analysis + url: http://edamontology.org/operation_2403 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: DNA + url: http://edamontology.org/topic_0654 + - term: Sequencing + url: http://edamontology.org/topic_3168 galaxy: - description: 'obiannotate: Adds/Edits sequence record annotations' title: obiannotate 1.2.13 @@ -12626,17 +15368,16 @@ publications: - title: 'obitools: A unix-inspired software package for DNA metabarcoding' url: http://www.ncbi.nlm.nih.gov/pubmed/25959493 - registry-link: obitools - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis - - DNA - - Sequencing + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 4.1.1--pyhdfd78af_0 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: ont-fast5-api @@ -12646,17 +15387,73 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: openms + biotools: openms bunya: '' description: Open source library and a collection of tools and interfaces for the analysis of mass spectrometry data. Includes over 200 standalone (TOPP) tools that can be combined to a workflow with the integrated workflow editor TOPPAS. Raw and intermediate mass spectrometry data can be visualised with the included viewer TOPPView. + edam-operations: + - term: Protein identification + url: http://edamontology.org/operation_3767 + - term: Parsing + url: http://edamontology.org/operation_1812 + - term: Data handling + url: http://edamontology.org/operation_2409 + - term: Chromatographic alignment + url: http://edamontology.org/operation_3628 + - term: Mass spectra calibration + url: http://edamontology.org/operation_3627 + - term: Formatting + url: http://edamontology.org/operation_0335 + - term: Protein quantification + url: http://edamontology.org/operation_3630 + - term: Retention time prediction + url: http://edamontology.org/operation_3633 + - term: Annotation + url: http://edamontology.org/operation_0226 + - term: Protein feature detection + url: http://edamontology.org/operation_3092 + - term: Isotope-coded protein label + url: http://edamontology.org/operation_3705 + - term: Label-free quantification + url: http://edamontology.org/operation_3634 + - term: iTRAQ + url: http://edamontology.org/operation_3639 + - term: Peptide identification + url: http://edamontology.org/operation_3631 + - term: Peak detection + url: http://edamontology.org/operation_3215 + - term: Mass spectrum visualisation + url: http://edamontology.org/operation_3694 + - term: Labeled quantification + url: http://edamontology.org/operation_3635 + - term: Splitting + url: http://edamontology.org/operation_3359 + - term: Spectral analysis + url: http://edamontology.org/operation_3214 + - term: Deisotoping + url: http://edamontology.org/operation_3629 + - term: Target-Decoy + url: http://edamontology.org/operation_3649 + - term: Prediction and recognition (protein) + url: http://edamontology.org/operation_3023 + - term: Comparison + url: http://edamontology.org/operation_2424 + - term: Standardisation and normalisation + url: http://edamontology.org/operation_3435 + edam-topics: + - term: Proteomics experiment + url: http://edamontology.org/topic_3520 + - term: Proteomics + url: http://edamontology.org/topic_0121 + - term: Metabolomics + url: http://edamontology.org/topic_3172 galaxy: - description: 'XTandemAdapter: Annotates MS/MS spectra using X! Tandem.' title: XTandemAdapter 2.8+galaxy0 @@ -12801,16 +15598,15 @@ url: https://doi.org/10.1038/nmeth.3959 - title: 'OpenMS and TOPP: open source software for LC-MS data analysis.' url: https://doi.org/10.1007/978-1-60761-987-1_23 - registry-link: openms - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics experiment - - Proteomics - - Metabolomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: orad @@ -12821,11 +15617,11 @@ - 2.6.1 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: OrthoFinder + biotools: OrthoFinder bunya: '' description: OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all @@ -12833,6 +15629,26 @@ It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. + edam-operations: + - term: Genome comparison + url: http://edamontology.org/operation_3209 + - term: Phylogenetic tree generation (from molecular sequences) + url: http://edamontology.org/operation_0540 + - term: Phylogenetic tree analysis + url: http://edamontology.org/operation_0324 + - term: Genome alignment + url: http://edamontology.org/operation_3182 + edam-topics: + - term: Phylogenetics + url: http://edamontology.org/topic_3293 + - term: Phylogenomics + url: http://edamontology.org/topic_0194 + - term: Bioinformatics + url: http://edamontology.org/topic_0091 + - term: Comparative genomics + url: http://edamontology.org/topic_0797 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'OrthoFinder: finds orthogroups in a set of proteomes' title: OrthoFinder 2.5.5+galaxy0 @@ -12849,18 +15665,15 @@ url: https://doi.org/10.1186/s13059-015-0721-2 - title: 10.1101/466201 url: https://doi.org/10.1101/466201 - registry-link: OrthoFinder - resource-description: .nan - resource-documentation: .nan - topics: - - Phylogenetics - - Phylogenomics - - Bioinformatics - - Comparative genomics - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Calculate community metrics: calculate community metrics from abundance data' @@ -12889,14 +15702,16 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 3.1.2 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://pandoc.org/ id: pandoc @@ -12906,11 +15721,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: pangolin + biotools: pangolin bunya: '' description: Pangolin is a deep-learning based method for predicting splice site strengths (for details, see Zeng and Li, Genome Biology 2022). It is available @@ -12918,6 +15733,28 @@ of interest; Pangolin will predict changes in splice site strength due to each variant, and return a file of the same format. Pangolin's models can also be used with custom sequences. + edam-operations: + - term: Splice site prediction + url: http://edamontology.org/operation_0433 + - term: Sequence merging + url: http://edamontology.org/operation_0232 + - term: Alternative splicing prediction + url: http://edamontology.org/operation_0264 + - term: Genotyping + url: http://edamontology.org/operation_3196 + - term: Variant classification + url: http://edamontology.org/operation_3225 + edam-topics: + - term: RNA splicing + url: http://edamontology.org/topic_3320 + - term: Genetic variation + url: http://edamontology.org/topic_0199 + - term: Gene transcripts + url: http://edamontology.org/topic_3512 + - term: RNA-Seq + url: http://edamontology.org/topic_3170 + - term: Exome sequencing + url: http://edamontology.org/topic_3676 galaxy: - description: 'Pangolin: Phylogenetic Assignment of Outbreak Lineages' title: Pangolin 4.3+galaxy2 @@ -12932,18 +15769,15 @@ publications: - title: Predicting RNA splicing from DNA sequence using Pangolin url: https://doi.org/10.1186/S13059-022-02664-4 - registry-link: pangolin - resource-description: .nan - resource-documentation: .nan - topics: - - RNA splicing - - Genetic variation - - Gene transcripts - - RNA-Seq - - Exome sequencing + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Parse parameter value: from dataset' title: Parse parameter value 0.1.0 @@ -12956,17 +15790,25 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: paraview + biotools: paraview bunya: '' description: "ParaView is an open-source, multi-platform data analysis and visualization\ \ application. ParaView users can quickly build visualizations to analyze their\ \ data using qualitative and quantitative techniques. The data exploration can\ \ be done interactively in 3D or programmatically using ParaView\u2019s batch\ \ processing capabilities." + edam-operations: + - term: Visualisation + url: http://edamontology.org/operation_0337 + edam-topics: + - term: Data visualisation + url: http://edamontology.org/topic_0092 + - term: Imaging + url: http://edamontology.org/topic_3382 galaxy: '' homepage: https://www.paraview.org/ id: paraview @@ -12986,15 +15828,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: paraview - resource-description: .nan - resource-documentation: .nan - topics: - - Data visualisation - - Imaging + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Parse mitochondrial blast: overlap-conscious coverage calculation between scaffold-accession number pairs from blast output' @@ -13008,16 +15850,28 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: parsnp + biotools: parsnp bunya: - 1.7.4--hdcf5f25_2 description: Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection. Parsnp was designed to work in tandem with Gingr, a flexible platform for visualizing genome alignments and phylogenetic trees. + edam-operations: + - term: SNP detection + url: http://edamontology.org/operation_0484 + - term: Genome alignment + url: http://edamontology.org/operation_3182 + edam-topics: + - term: DNA polymorphism + url: http://edamontology.org/topic_2885 + - term: Phylogenetics + url: http://edamontology.org/topic_3293 + - term: Structure analysis + url: http://edamontology.org/topic_0081 galaxy: '' homepage: https://github.com/marbl/parsnp id: parsnp @@ -13027,14 +15881,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: parsnp - resource-description: .nan - resource-documentation: .nan - topics: - - DNA polymorphism - - Phylogenetics - - Structure analysis + resources: + - title: .nan + url: .nan - biocontainers: pathview + biotools: pathview bunya: '' description: Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. @@ -13042,6 +15893,18 @@ pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. + edam-operations: + - term: Pathway or network analysis + url: http://edamontology.org/operation_2497 + - term: Pathway or network visualisation + url: http://edamontology.org/operation_3083 + edam-topics: + - term: Molecular interactions, pathways and networks + url: http://edamontology.org/topic_0602 + - term: Systems biology + url: http://edamontology.org/topic_2259 + - term: Data visualisation + url: http://edamontology.org/topic_0092 galaxy: - description: 'Pathview: for pathway based data integration and visualization' title: Pathview 1.34.0+galaxy0 @@ -13057,14 +15920,11 @@ - title: 'Pathview: An R/Bioconductor package for pathway-based data integration and visualization' url: https://doi.org/10.1093/bioinformatics/btt285 - registry-link: pathview - resource-description: .nan - resource-documentation: .nan - topics: - - Molecular interactions, pathways and networks - - Systems biology - - Data visualisation + resources: + - title: .nan + url: .nan - biocontainers: pavian + biotools: pavian bunya: '' description: Web application for exploring metagenomics classification results, with a special focus on infectious disease diagnosis. Pinpointing pathogens in @@ -13072,6 +15932,16 @@ contaminants as well as many non-pathogenic microbiota. Researchers can analyze, display and transform results from the Kraken and Centrifuge classifiers using interactive tables, heatmaps and flow diagrams. + edam-operations: + - term: Annotation + url: http://edamontology.org/operation_0226 + - term: Taxonomic classification + url: http://edamontology.org/operation_3460 + edam-topics: + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Model organisms + url: http://edamontology.org/topic_0621 galaxy: - description: 'Pavian: Interactive analysis of metagenomics data' title: Pavian 1.0 @@ -13086,15 +15956,25 @@ publications: - title: 10.1101/084715 url: https://doi.org/10.1101/084715 - registry-link: pavian - resource-description: .nan - resource-documentation: .nan - topics: - - Metagenomics - - Model organisms + resources: + - title: .nan + url: .nan - biocontainers: pblat + biotools: pblat bunya: '' description: Multithread blat algorithm speeding up aligning sequences to genomes. + edam-operations: + - term: Protein threading + url: http://edamontology.org/operation_0302 + - term: Read mapping + url: http://edamontology.org/operation_3198 + edam-topics: + - term: RNA-seq + url: http://edamontology.org/topic_3170 + - term: Mapping + url: http://edamontology.org/topic_0102 + - term: Gene transcripts + url: http://edamontology.org/topic_3512 galaxy: '' homepage: https://github.com/icebert/pblat id: pblat @@ -13108,17 +15988,34 @@ - title: 'pblat: A multithread blat algorithm speeding up aligning sequences to genomes' url: https://doi.org/10.1186/s12859-019-2597-8 - registry-link: pblat - resource-description: .nan - resource-documentation: .nan - topics: - - RNA-seq - - Mapping - - Gene transcripts + resources: + - title: .nan + url: .nan - biocontainers: seqcode + biotools: seqcode bunya: '' description: Productive visualization of high-throughput sequencing data using the SeqCode open portable platform. + edam-operations: + - term: Visualisation + url: http://edamontology.org/operation_0337 + - term: Peak calling + url: http://edamontology.org/operation_3222 + - term: Essential dynamics + url: http://edamontology.org/operation_3891 + - term: Phylogenetic footprinting + url: http://edamontology.org/operation_0327 + edam-topics: + - term: ChIP-seq + url: http://edamontology.org/topic_3169 + - term: RNA-Seq + url: http://edamontology.org/topic_3170 + - term: Epigenetics + url: http://edamontology.org/topic_3295 + - term: Methylated DNA immunoprecipitation + url: http://edamontology.org/topic_3674 + - term: Transcription factors and regulatory sites + url: http://edamontology.org/topic_0749 galaxy: - description: 'Paired-end histogram: of insert size frequency' title: Paired-end histogram 1.0.1 @@ -13134,21 +16031,22 @@ - title: Productive visualization of high-throughput sequencing data using the SeqCode open portable platform url: https://doi.org/10.1038/S41598-021-98889-7 - registry-link: seqcode - resource-description: .nan - resource-documentation: .nan - topics: - - ChIP-seq - - RNA-Seq - - Epigenetics - - Methylated DNA immunoprecipitation - - Transcription factors and regulatory sites + resources: + - title: .nan + url: .nan - biocontainers: pear + biotools: pear bunya: - 0.9.6--h9d449c0_10 description: Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. + edam-operations: + - term: Sequence merging + url: http://edamontology.org/operation_0232 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: - description: 'Pear: Paired-End read merger' title: Pear 0.9.6.2 @@ -13163,14 +16061,15 @@ publications: - title: 'PEAR: A fast and accurate Illumina Paired-End reAd mergeR' url: https://doi.org/10.1093/bioinformatics/btt593 - registry-link: pear - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'PepPointer: classify genomic location of peptides' title: PepPointer 0.1.3+galaxy1 @@ -13183,11 +16082,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: peptideshaker + biotools: peptideshaker bunya: '' description: PeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting @@ -13195,6 +16094,28 @@ and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data + edam-operations: + - term: PTM localisation + url: http://edamontology.org/operation_3755 + - term: Protein identification + url: http://edamontology.org/operation_3767 + - term: Structure visualisation + url: http://edamontology.org/operation_0570 + - term: Validation + url: http://edamontology.org/operation_2428 + - term: Peptide identification + url: http://edamontology.org/operation_3631 + - term: Mass spectrum visualisation + url: http://edamontology.org/operation_3694 + - term: Enrichment analysis + url: http://edamontology.org/operation_3501 + edam-topics: + - term: Proteomics + url: http://edamontology.org/topic_0121 + - term: Proteomics experiment + url: http://edamontology.org/topic_3520 + - term: Proteome + url: http://edamontology.org/topic_0644 galaxy: - description: 'FastaCLI: Appends decoy sequences to FASTA files' title: FastaCLI 4.0.41+galaxy1 @@ -13222,16 +16143,15 @@ - title: 'PeptideShaker enables reanalysis of MS-derived proteomics data sets: To the editor' url: https://doi.org/10.1038/nbt.3109 - registry-link: peptideshaker - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics - - Proteomics experiment - - Proteome + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Peptide Genomic Coordinate: Get Peptide''s genomic coordinate using mzsqlite DB and genomic mapping sqlite DB' @@ -13245,13 +16165,35 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: percolator + biotools: percolator bunya: '' description: Semi-supervised learning for peptide identification from MS/MS data. + edam-operations: + - term: Protein fragment weight comparison + url: http://edamontology.org/operation_2929 + - term: Protein identification + url: http://edamontology.org/operation_3767 + - term: Blind peptide database search + url: http://edamontology.org/operation_3647 + - term: Peptide identification + url: http://edamontology.org/operation_3631 + - term: Target-Decoy + url: http://edamontology.org/operation_3649 + - term: Validation of peptide-spectrum matches + url: http://edamontology.org/operation_3648 + edam-topics: + - term: Proteomics + url: http://edamontology.org/topic_0121 + - term: Proteomics experiment + url: http://edamontology.org/topic_3520 + - term: Statistics and probability + url: http://edamontology.org/topic_2269 + - term: Machine learning + url: http://edamontology.org/topic_3474 galaxy: - description: 'Search engine output to Pin converter: to create Percolator input files' @@ -13277,17 +16219,15 @@ - title: Semi-supervised learning for peptide identification from shotgun proteomics datasets url: http://www.ncbi.nlm.nih.gov/pubmed/17952086 - registry-link: percolator - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics - - Proteomics experiment - - Statistics and probability - - Machine learning + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: perllib @@ -13298,14 +16238,20 @@ - v5.26.3 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: pfamscan + biotools: pfamscan bunya: '' description: This tool is used to search a FASTA sequence against a library of Pfam HMM. + edam-operations: + - term: Protein sequence analysis + url: http://edamontology.org/operation_2479 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'PfamScan: search a FASTA sequence against a library of Pfam HMM' title: PfamScan 1.6+galaxy0 @@ -13318,15 +16264,34 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: pfamscan - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: pharokka + biotools: pharokka bunya: '' description: Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. + edam-operations: + - term: Genome annotation + url: http://edamontology.org/operation_0362 + - term: Antimicrobial resistance prediction + url: http://edamontology.org/operation_3482 + - term: tRNA gene prediction + url: http://edamontology.org/operation_0464 + - term: Formatting + url: http://edamontology.org/operation_0335 + - term: Sequence assembly + url: http://edamontology.org/operation_0310 + edam-topics: + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Sequence sites, features and motifs + url: http://edamontology.org/topic_0160 + - term: Workflows + url: http://edamontology.org/topic_0769 + - term: Functional, regulatory and non-coding RNA + url: http://edamontology.org/topic_0659 galaxy: - description: 'pharokka: Rapid standardised annotation tool for bacteriophage genomes and metagenomes' @@ -13342,17 +16307,15 @@ publications: - title: 'Pharokka: a fast scalable bacteriophage annotation tool' url: https://doi.org/10.1093/BIOINFORMATICS/BTAC776 - registry-link: pharokka - resource-description: .nan - resource-documentation: .nan - topics: - - Metagenomics - - Sequence sites, features and motifs - - Workflows - - Functional, regulatory and non-coding RNA + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Phinch Visualisation: ' title: Phinch Visualisation 0.1 @@ -13365,13 +16328,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://www.php.net/ id: php @@ -13382,14 +16347,28 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: phyloseq + biotools: phyloseq bunya: '' description: Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. + edam-operations: + - term: Deposition + url: http://edamontology.org/operation_3431 + - term: Analysis + url: http://edamontology.org/operation_2945 + - term: Visualisation + url: http://edamontology.org/operation_0337 + edam-topics: + - term: Microbiology + url: http://edamontology.org/topic_3301 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Metagenomics + url: http://edamontology.org/topic_3174 galaxy: - description: 'Phyloseq Biom Filtering: biom file filter' title: Phyloseq Biom Filtering 1.22.3.2 @@ -13408,16 +16387,23 @@ - title: 'Phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data' url: https://doi.org/10.1371/journal.pone.0061217 - registry-link: phyloseq - resource-description: .nan - resource-documentation: .nan - topics: - - Microbiology - - Sequence analysis - - Metagenomics + resources: + - title: .nan + url: .nan - biocontainers: phyml + biotools: phyml bunya: '' description: Phylogenetic estimation software using Maximum Likelihood + edam-operations: + - term: Phylogenetic tree generation (maximum likelihood and Bayesian methods) + url: http://edamontology.org/operation_0547 + edam-topics: + - term: Phylogenetics + url: http://edamontology.org/topic_3293 + - term: Bioinformatics + url: http://edamontology.org/topic_0091 + - term: Phylogenetics + url: http://edamontology.org/topic_3293 galaxy: - description: 'PhyML: Phylogeny software based on the maximum-likelihood method' title: PhyML 3.3.20220408+galaxy0 @@ -13440,19 +16426,24 @@ url: https://doi.org/10.1080/10635150600755453 - title: 10.1093/nar/gki352 url: https://doi.org/10.1093/nar/gki352 - registry-link: phyml - resource-description: .nan - resource-documentation: .nan - topics: - - Phylogenetics - - Bioinformatics - - Phylogenetics + resources: + - title: .nan + url: .nan - biocontainers: picard_tools + biotools: picard_tools bunya: - 2.25.1-java-11 description: A set of command line tools for manipulating high-throughput sequencing (HTS) data in formats such as SAM/BAM/CRAM and VCF. Available as a standalone program or within the GATK4 program. + edam-operations: + - term: Genetic variation analysis + url: http://edamontology.org/operation_3197 + edam-topics: + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Data management + url: http://edamontology.org/topic_3071 galaxy: - description: 'FixMateInformation: ensure that all mate-pair information is in sync between each read and it''s mate pair' @@ -13570,20 +16561,37 @@ nci-gadi: '' nci-if89: - 2.27.4 + - 3.1.1 pawsey: '' publications: '' - registry-link: picard_tools - resource-description: .nan - resource-documentation: .nan - topics: - - Sequencing - - Data management + resources: + - title: .nan + url: .nan - biocontainers: picrust + biotools: picrust bunya: '' description: PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. + edam-operations: + - term: Phylogenetic reconstruction + url: http://edamontology.org/operation_3478 + - term: Expression analysis + url: http://edamontology.org/operation_2495 + - term: Genome annotation + url: http://edamontology.org/operation_0362 + - term: DNA barcoding + url: http://edamontology.org/operation_3200 + edam-topics: + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Microbial ecology + url: http://edamontology.org/topic_3697 + - term: Functional, regulatory and non-coding RNA + url: http://edamontology.org/topic_0659 + - term: Metagenomic sequencing + url: http://edamontology.org/topic_3837 galaxy: - description: 'Categorize: by collapsing hierarchical data to a specified functional level' @@ -13618,19 +16626,33 @@ - title: Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences url: https://doi.org/10.1038/nbt.2676 - registry-link: picrust - resource-description: .nan - resource-documentation: .nan - topics: - - Metagenomics - - Microbial ecology - - Functional, regulatory and non-coding RNA - - Metagenomic sequencing + resources: + - title: .nan + url: .nan - biocontainers: picrust2 + biotools: picrust2 bunya: '' description: PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. + edam-operations: + - term: Phylogenetic reconstruction + url: http://edamontology.org/operation_3478 + - term: Expression analysis + url: http://edamontology.org/operation_2495 + - term: Rarefaction + url: http://edamontology.org/operation_3797 + - term: Pathway analysis + url: http://edamontology.org/operation_3928 + edam-topics: + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Microbiology + url: http://edamontology.org/topic_3301 + - term: Phylogenetics + url: http://edamontology.org/topic_3293 + - term: Metagenomic sequencing + url: http://edamontology.org/topic_3837 galaxy: - description: 'PICRUSt2 Add descriptions: column to a function abundance table' title: PICRUSt2 Add descriptions 2.5.1+galaxy0 @@ -13665,17 +16687,15 @@ publications: - title: 10.1038/s41587-020-0548-6 url: https://doi.org/10.1038/s41587-020-0548-6 - registry-link: picrust2 - resource-description: .nan - resource-documentation: .nan - topics: - - Metagenomics - - Microbiology - - Phylogenetics - - Metagenomic sequencing + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Pileup-to-Interval: condenses pileup format into ranges of bases' title: Pileup-to-Interval 1.0.3 @@ -13688,13 +16708,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Filter pileup: on coverage and SNPs' title: Filter pileup 1.0.2 @@ -13707,14 +16729,20 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: pilon + biotools: pilon bunya: '' description: Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. + edam-operations: + - term: Sequence assembly + url: http://edamontology.org/operation_0310 + edam-topics: + - term: Assembly + url: http://edamontology.org/topic_0196 galaxy: - description: 'pilon: An automated genome assembly improvement and variant detection tool' @@ -13731,12 +16759,11 @@ - title: 'Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement' url: https://doi.org/10.1371/journal.pone.0112963 - registry-link: pilon - resource-description: .nan - resource-documentation: .nan - topics: - - Assembly + resources: + - title: .nan + url: .nan - biocontainers: PIPE-T + biotools: PIPE-T bunya: '' description: 'PIPE-T is a Galaxy Workflow for processing and analyzing miR expression profiles by RTqPCR. @@ -13748,6 +16775,26 @@ as those without any programming or development expertise, to perform complex analysis in a simple to use, transparent, accessible, reproducible, and user-friendly environment' + edam-operations: + - term: Essential dynamics + url: http://edamontology.org/operation_3891 + - term: Quantification + url: http://edamontology.org/operation_3799 + - term: Standardisation and normalisation + url: http://edamontology.org/operation_3435 + - term: Imputation + url: http://edamontology.org/operation_3557 + - term: Parsing + url: http://edamontology.org/operation_1812 + edam-topics: + - term: PCR experiment + url: http://edamontology.org/topic_3519 + - term: Transcriptomics + url: http://edamontology.org/topic_3308 + - term: Biomarkers + url: http://edamontology.org/topic_3360 + - term: Microarray experiment + url: http://edamontology.org/topic_3518 galaxy: - description: 'PIPE-T: A tool for analyzing RTqPCR expression data' title: PIPE-T 1.0 @@ -13762,17 +16809,15 @@ publications: - title: 'PIPE-T: a new Galaxy tool for the analysis of RT-qPCR expression data' url: https://doi.org/10.1038/S41598-019-53155-9 - registry-link: PIPE-T - resource-description: .nan - resource-documentation: .nan - topics: - - PCR experiment - - Transcriptomics - - Biomarkers - - Microarray experiment + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'PlasFlow: Prediction of plasmid sequences in metagenomic contigs' title: PlasFlow 1.1.0+galaxy0 @@ -13785,16 +16830,22 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: plink + biotools: plink bunya: - 2.00a3.6-gcc-11.3.0 description: Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. + edam-operations: + - term: Genetic variation analysis + url: http://edamontology.org/operation_3197 + edam-topics: + - term: GWAS study + url: http://edamontology.org/topic_3517 galaxy: '' homepage: http://zzz.bwh.harvard.edu/plink/ id: plink @@ -13808,19 +16859,20 @@ - title: 'PLINK: A tool set for whole-genome association and population-based linkage analyses' url: https://doi.org/10.1086/519795 - registry-link: plink - resource-description: .nan - resource-documentation: .nan - topics: - - GWAS study + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Plot confusion matrix, precision, recall and ROC and AUC curves: of tabular data' - title: Plot confusion matrix, precision, recall and ROC and AUC curves 0.2 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fplotly_ml_performance_plots%2Fplotly_ml_performance_plots%2F0.2 + title: Plot confusion matrix, precision, recall and ROC and AUC curves 0.3 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fplotly_ml_performance_plots%2Fplotly_ml_performance_plots%2F0.3 - description: 'Parallel Coordinates Plot: of tabular data' title: Parallel Coordinates Plot 0.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fplotly_parallel_coordinates_plot%2Fplotly_parallel_coordinates_plot%2F0.2 @@ -13835,13 +16887,19 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: pnetcdf + biotools: pnetcdf bunya: '' description: 'PnetCDF: A Parallel I/O Library for NetCDF File Access' + edam-operations: + - term: Aggregation + url: http://edamontology.org/operation_3436 + edam-topics: + - term: Computer science + url: http://edamontology.org/topic_3316 galaxy: '' homepage: https://parallel-netcdf.github.io/ id: pnetcdf @@ -13854,14 +16912,15 @@ publications: - title: 10.1109/SC.2003.10053 url: https://doi.org/10.1109/SC.2003.10053 - registry-link: pnetcdf - resource-description: .nan - resource-documentation: .nan - topics: - - Computer science + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Poisson two-sample test: ' title: Poisson two-sample test 1.0.0 @@ -13874,13 +16933,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Porechop: adapter trimmer for Oxford Nanopore reads' title: Porechop 0.2.4+galaxy0 @@ -13893,14 +16954,22 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: poretools + biotools: poretools bunya: '' description: Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. + edam-operations: + - term: Nucleic acid sequence analysis + url: http://edamontology.org/operation_2478 + edam-topics: + - term: DNA + url: http://edamontology.org/topic_0654 + - term: Sequencing + url: http://edamontology.org/topic_3168 galaxy: - description: 'Extract nanopore events: from a set of sequencing reads' title: Extract nanopore events 0.6.1a1.1 @@ -13952,17 +17021,21 @@ publications: - title: 'Poretools: A toolkit for analyzing nanopore sequence data' url: http://www.ncbi.nlm.nih.gov/pubmed/25143291 - registry-link: poretools - resource-description: .nan - resource-documentation: .nan - topics: - - DNA - - Sequencing + resources: + - title: .nan + url: .nan - biocontainers: clstutils + biotools: clstutils bunya: - 1.1.alpha19 description: Tools for performing taxonomic assignment based on phylogeny using pplacer and clst. + edam-operations: + - term: Taxonomic classification + url: http://edamontology.org/operation_3460 + edam-topics: + - term: Taxonomy + url: http://edamontology.org/topic_0637 galaxy: '' homepage: http://bioconductor.org/packages/release/bioc/html/clstutils.html id: pplacer @@ -13974,14 +17047,15 @@ publications: - title: Orchestrating high-throughput genomic analysis with Bioconductor url: https://doi.org/10.1038/nmeth.3252 - registry-link: clstutils - resource-description: .nan - resource-documentation: .nan - topics: - - Taxonomy + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'PretextMap: converts SAM or BAM files into genome contact maps' title: PretextMap 0.1.9+galaxy1 @@ -13994,13 +17068,19 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: pretextview + biotools: pretextview bunya: '' description: Pretext is an OpenGL-powered pretext contact map viewer. + edam-operations: + - term: Scaffolding + url: http://edamontology.org/operation_3216 + edam-topics: + - term: Mapping + url: http://edamontology.org/topic_0102 galaxy: - description: 'Pretext Snapshot: image generator for Pretext contact maps' title: Pretext Snapshot 0.0.3+galaxy2 @@ -14013,12 +17093,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: pretextview - resource-description: .nan - resource-documentation: .nan - topics: - - Mapping + resources: + - title: .nan + url: .nan - biocontainers: gmv + biotools: gmv bunya: - 2.6.3-gcccore-10.3.0 - 2.6.3-gcccore-11.3.0 (D) @@ -14029,6 +17108,16 @@ a majority of the highest-scoring PRODIGAL selected sites coincide. If such a position is found, it is accepted, and the predictions are changed for the outlying genes. + edam-operations: + - term: Gene prediction + url: http://edamontology.org/operation_2454 + edam-topics: + - term: DNA + url: http://edamontology.org/topic_0654 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Nucleic acid sites, features and motifs + url: http://edamontology.org/topic_3511 galaxy: '' homepage: https://code.google.com/p/gmv/ id: prodigal @@ -14041,14 +17130,11 @@ publications: - title: Genome majority vote improves gene predictions url: http://www.ncbi.nlm.nih.gov/pubmed/22131910 - registry-link: gmv - resource-description: .nan - resource-documentation: .nan - topics: - - DNA - - Sequence analysis - - Nucleic acid sites, features and motifs + resources: + - title: .nan + url: .nan - biocontainers: profia + biotools: profia bunya: '' description: Flow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA-HRMS data, however, @@ -14056,6 +17142,12 @@ separation, or handle low resolution data only. Here we present the package that implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) and generates the peak table. + edam-operations: + - term: Peak calling + url: http://edamontology.org/operation_3222 + edam-topics: + - term: Metabolomics + url: http://edamontology.org/topic_3172 galaxy: - description: 'proFIA: Preprocessing of FIA-HRMS data' title: proFIA 3.1.0 @@ -14070,14 +17162,15 @@ publications: - title: Orchestrating high-throughput genomic analysis with Bioconductor url: https://doi.org/10.1038/nmeth.3252 - registry-link: profia - resource-description: .nan - resource-documentation: .nan - topics: - - Metabolomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: progressbar2 @@ -14088,16 +17181,30 @@ - 4.2.0 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: prokka + biotools: prokka bunya: - 1.14.5-gompi-2021a - 1.14.5-gompi-2022a (D) description: Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. + edam-operations: + - term: Gene prediction + url: http://edamontology.org/operation_2454 + - term: Coding region prediction + url: http://edamontology.org/operation_0436 + - term: Genome annotation + url: http://edamontology.org/operation_0362 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Model organisms + url: http://edamontology.org/topic_0621 + - term: Virology + url: http://edamontology.org/topic_0781 galaxy: - description: 'Prokka: Prokaryotic genome annotation' title: Prokka 1.14.6+galaxy1 @@ -14112,16 +17219,15 @@ publications: - title: 10.1093/bioinformatics/btu153 url: https://doi.org/10.1093/bioinformatics/btu153 - registry-link: prokka - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Model organisms - - Virology + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'proportional venn: from 2-3 sets' title: proportional venn 0.5 @@ -14134,13 +17240,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://anaconda.org/bioconda/ucsc-pslcdnafilter id: pslcdnafilter @@ -14151,11 +17259,11 @@ - '0' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: purge_dups + biotools: purge_dups bunya: '' description: 'Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: @@ -14166,6 +17274,16 @@ be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences' + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: Read binning + url: http://edamontology.org/operation_3798 + - term: Scaffolding + url: http://edamontology.org/operation_3216 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: - description: 'Purge overlaps: and haplotigs in an assembly based on read depth (purge_dups)' @@ -14181,16 +17299,17 @@ publications: - title: 10.1101/729962 url: https://doi.org/10.1101/729962 - registry-link: purge_dups - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 0.3.18-foss-2021a - 0.3.18-foss-2022a (D) description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: pybigwig @@ -14200,15 +17319,27 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: pycoqc + biotools: pycoqc bunya: - 2.5.2-foss-2021a description: PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. + edam-operations: + - term: Sequencing quality control + url: http://edamontology.org/operation_3218 + - term: Statistical calculation + url: http://edamontology.org/operation_2238 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Data quality management + url: http://edamontology.org/topic_3572 + - term: Sequencing + url: http://edamontology.org/topic_3168 galaxy: - description: 'Pycoqc: quality control for Nanopore sequencing data' title: Pycoqc 2.5.2+galaxy0 @@ -14221,14 +17352,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: pycoqc - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis - - Data quality management - - Sequencing + resources: + - title: .nan + url: .nan - biocontainers: pygenometracks + biotools: pygenometracks bunya: '' description: 'reproducible plots for multivariate genomic data sets. @@ -14238,6 +17366,18 @@ pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.' + edam-operations: + - term: Visualisation + url: http://edamontology.org/operation_0337 + - term: Formatting + url: http://edamontology.org/operation_0335 + edam-topics: + - term: Model organisms + url: http://edamontology.org/topic_0621 + - term: Imaging + url: http://edamontology.org/topic_3382 + - term: Workflows + url: http://edamontology.org/topic_0769 galaxy: - description: 'pyGenomeTracks: plot genomic data tracks' title: pyGenomeTracks 3.8+galaxy2 @@ -14252,16 +17392,15 @@ publications: - title: 'pyGenomeTracks: reproducible plots for multivariate genomic datasets' url: https://doi.org/10.1093/BIOINFORMATICS/BTAA692 - registry-link: pygenometracks - resource-description: .nan - resource-documentation: .nan - topics: - - Model organisms - - Imaging - - Workflows + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'PyProphet merge: Merge multiple osw files' title: PyProphet merge 2.1.4.0 @@ -14284,15 +17423,25 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: pysam + biotools: pysam bunya: - 0.16.0.1-gcc-10.3.0 - 0.19.1-gcc-11.3.0 (D) description: A Python module for reading and manipulating SAM/BAM/VCF/BCF files. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + - term: Sequence file editing + url: http://edamontology.org/operation_2121 + edam-topics: + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Mapping + url: http://edamontology.org/topic_0102 galaxy: '' homepage: https://github.com/pysam-developers/pysam id: pysam @@ -14304,16 +17453,20 @@ publications: - title: The Sequence Alignment/Map format and SAMtools url: https://doi.org/10.1093/bioinformatics/btp352 - registry-link: pysam - resource-description: .nan - resource-documentation: .nan - topics: - - Sequencing - - Mapping + resources: + - title: .nan + url: .nan - biocontainers: pytorch + biotools: pytorch bunya: '' description: PyTorch is an optimized tensor library for deep learning using GPUs and CPUs. + edam-operations: '' + edam-topics: + - term: Machine learning + url: http://edamontology.org/topic_3474 + - term: Computer science + url: http://edamontology.org/topic_3316 galaxy: '' homepage: https://pytorch.org/ id: pytorch @@ -14328,17 +17481,33 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: pytorch - resource-description: .nan - resource-documentation: .nan - topics: - - Machine learning - - Computer science + resources: + - title: .nan + url: .nan - biocontainers: qiime2 + biotools: qiime2 bunya: - '2022.8' description: "QIIME 2\u2122 is a next-generation microbiome bioinformatics platform\ \ that is extensible, free, open source, and community developed." + edam-operations: + - term: Demultiplexing + url: http://edamontology.org/operation_3933 + - term: Visualisation + url: http://edamontology.org/operation_0337 + - term: Taxonomic classification + url: http://edamontology.org/operation_3460 + - term: Phylogenetic analysis + url: http://edamontology.org/operation_0324 + edam-topics: + - term: Microbial ecology + url: http://edamontology.org/topic_3697 + - term: Phylogeny + url: http://edamontology.org/topic_0084 + - term: Metatranscriptomics + url: http://edamontology.org/topic_3941 + - term: Metagenomics + url: http://edamontology.org/topic_3174 galaxy: - description: 'qiime2 tools import: Import data into a QIIME 2 artifact' title: qiime2 tools import 2023.5.0+dist.h193f7cc9.3 @@ -14930,17 +18099,15 @@ - title: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 url: https://doi.org/10.1038/s41587-019-0209-9 - registry-link: qiime2 - resource-description: .nan - resource-documentation: .nan - topics: - - Microbial ecology - - Phylogeny - - Metatranscriptomics - - Metagenomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Boxplot: of quality statistics' title: Boxplot 1.0.1 @@ -14953,15 +18120,21 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: qualimap + biotools: qualimap bunya: '' description: Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. + edam-operations: + - term: Sequencing quality control + url: http://edamontology.org/operation_3218 + edam-topics: + - term: Data quality management + url: http://edamontology.org/topic_3572 galaxy: - description: 'QualiMap BamQC: ' title: QualiMap BamQC 2.2.2d+galaxy3 @@ -14985,12 +18158,11 @@ publications: - title: '22914218' url: http://www.ncbi.nlm.nih.gov/pubmed/22914218 - registry-link: qualimap - resource-description: .nan - resource-documentation: .nan - topics: - - Data quality management + resources: + - title: .nan + url: .nan - biocontainers: quasitools + biotools: quasitools bunya: '' description: 'A Collection of Tools for Viral Quasispecies Analysis | Abstract Summary quasitools is a collection of newly-developed, open-source tools for analyzing @@ -15002,6 +18174,20 @@ licensed under the Apache License, Version 2.0. The source code, documentation, and file specifications are available at: https: phac-nml.github.io quasitools Contact gary.vandomselaar@canada.ca' + edam-operations: + - term: Sequence trimming + url: http://edamontology.org/operation_3192 + - term: Genotyping + url: http://edamontology.org/operation_3196 + - term: Base-calling + url: http://edamontology.org/operation_3185 + edam-topics: + - term: Virology + url: http://edamontology.org/topic_0781 + - term: Small molecules + url: http://edamontology.org/topic_0154 + - term: Sequencing + url: http://edamontology.org/topic_3168 galaxy: - description: 'Consensus Sequence: Generate a consensus sequence from a BAM file' title: Consensus Sequence 0.7.0+galaxy1 @@ -15052,19 +18238,24 @@ publications: - title: 10.1101/733238 url: https://doi.org/10.1101/733238 - registry-link: quasitools - resource-description: .nan - resource-documentation: .nan - topics: - - Virology - - Small molecules - - Sequencing + resources: + - title: .nan + url: .nan - biocontainers: quast + biotools: quast bunya: - 5.0.2-foss-2021a - 5.2.0-foss-2022a (D) description: "QUAST stands for QUality ASsessment Tool. \nIt evaluates a quality\ \ of genome assemblies by computing various metrics and providing nice reports." + edam-operations: + - term: Visualisation + url: http://edamontology.org/operation_0337 + - term: Sequence assembly validation + url: http://edamontology.org/operation_3180 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: - description: 'Quast: Genome assembly Quality' title: Quast 5.2.0+galaxy1 @@ -15076,22 +18267,36 @@ nci-gadi: '' nci-if89: - 5.1.0rc1 + - 5.2.0 pawsey: '' publications: - title: 'QUAST: Quality assessment tool for genome assemblies' url: http://www.ncbi.nlm.nih.gov/pubmed/23422339 - registry-link: quast - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly + resources: + - title: .nan + url: .nan - biocontainers: Query_Tabular + biotools: Query_Tabular bunya: '' description: Query Tabular is a Galaxy-based tool which manipulates tabular files. Query Tabular automatically creates a SQLite database directly from a tabular file within a Galaxy workflow. The SQLite database can be saved to the Galaxy history, and further process to generate tabular outputs containing desired information and formatting. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + - term: Parsing + url: http://edamontology.org/operation_1812 + - term: Query and retrieval + url: http://edamontology.org/operation_0224 + - term: Filtering + url: http://edamontology.org/operation_3695 + edam-topics: + - term: Bioinformatics + url: http://edamontology.org/topic_0091 + - term: Workflows + url: http://edamontology.org/topic_0769 galaxy: - description: 'Query Tabular: using sqlite sql' title: Query Tabular 3.3.1 @@ -15106,18 +18311,30 @@ publications: - title: 'Improve your Galaxy text life: The Query Tabular Tool' url: https://doi.org/10.12688/f1000research.16450.2 - registry-link: Query_Tabular - resource-description: .nan - resource-documentation: .nan - topics: - - Bioinformatics - - Workflows + resources: + - title: .nan + url: .nan - biocontainers: r + biotools: r bunya: - 4.1.0-foss-2021a - 4.2.1-foss-2021a - 4.2.1-foss-2022a (D) description: Free software environment for statistical computing and graphics. + edam-operations: + - term: Analysis + url: http://edamontology.org/operation_2945 + - term: Data handling + url: http://edamontology.org/operation_2409 + - term: Visualisation + url: http://edamontology.org/operation_0337 + edam-topics: + - term: Mathematics + url: http://edamontology.org/topic_3315 + - term: Data architecture, analysis and design + url: http://edamontology.org/topic_3365 + - term: Statistics and probability + url: http://edamontology.org/topic_2269 galaxy: '' homepage: http://www.r-project.org/ id: r @@ -15133,16 +18350,15 @@ publications: - title: 10.11120/msor.2001.01010023 url: https://doi.org/10.11120/msor.2001.01010023 - registry-link: r - resource-description: .nan - resource-documentation: .nan - topics: - - Mathematics - - Data architecture, analysis and design - - Statistics and probability + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Initial processing using RaceID: performs filtering, normalisation, and confounder removal to generate a normalised and filtered count matrix of @@ -15172,11 +18388,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: Racon + biotools: Racon bunya: '' description: 'Consensus module for raw de novo DNA assembly of long uncorrected reads @@ -15189,6 +18405,16 @@ and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.' + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: Mapping assembly + url: http://edamontology.org/operation_0523 + edam-topics: + - term: Whole genome sequencing + url: http://edamontology.org/topic_3673 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: - description: 'Racon: Consensus module for raw de novo DNA assembly of long uncorrected reads' @@ -15206,16 +18432,26 @@ - title: 'Constructing a reference genome in a single lab: The possibility to use oxford nanopore technology' url: https://doi.org/10.3390/PLANTS8080270 - registry-link: Racon - resource-description: .nan - resource-documentation: .nan - topics: - - Whole genome sequencing - - Sequence assembly + resources: + - title: .nan + url: .nan - biocontainers: ramclustr + biotools: ramclustr bunya: '' description: A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. + edam-operations: + - term: Imputation + url: http://edamontology.org/operation_3557 + - term: Standardisation and normalisation + url: http://edamontology.org/operation_3435 + - term: Clustering + url: http://edamontology.org/operation_3432 + - term: Correlation + url: http://edamontology.org/operation_3465 + edam-topics: + - term: Metabolomics + url: http://edamontology.org/topic_3172 galaxy: - description: 'RAMClustR define experiment: Definition of experimental design used for record keeping and writing spectra data.' @@ -15236,12 +18472,11 @@ - title: 'RAMClust: A novel feature clustering method enables spectral-matching-based annotation for metabolomics data' url: https://doi.org/10.1021/ac501530d - registry-link: ramclustr - resource-description: .nan - resource-documentation: .nan - topics: - - Metabolomics + resources: + - title: .nan + url: .nan - biocontainers: ratatosk + biotools: ratatosk bunya: - 0.7.6.3--h43eeafb_2 description: "Ratatosk \u2013 Hybrid error correction of long reads enables accurate\ @@ -15249,6 +18484,24 @@ \ using colored de Bruijn graphs.\n\nRatatosk is a phased error correction tool\ \ for erroneous long reads based on compacted and colored de Bruijn graphs built\ \ from accurate short reads." + edam-operations: + - term: De-novo assembly + url: http://edamontology.org/operation_0524 + - term: Sequencing error detection + url: http://edamontology.org/operation_3195 + - term: Variant calling + url: http://edamontology.org/operation_3227 + - term: Phasing + url: http://edamontology.org/operation_3454 + - term: Read binning + url: http://edamontology.org/operation_3798 + edam-topics: + - term: DNA polymorphism + url: http://edamontology.org/topic_2885 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Whole genome sequencing + url: http://edamontology.org/topic_3673 galaxy: '' homepage: https://github.com/DecodeGenetics/Ratatosk id: ratatosk @@ -15260,16 +18513,15 @@ publications: - title: 10.1101/2020.07.15.204925 url: https://doi.org/10.1101/2020.07.15.204925 - registry-link: ratatosk - resource-description: .nan - resource-documentation: .nan - topics: - - DNA polymorphism - - Sequence assembly - - Whole genome sequencing + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Ratmine: server' title: Ratmine 1.0.0 @@ -15282,20 +18534,34 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: raven + biotools: raven bunya: '' description: 'a de novo genome assembler for long reads. Raven is a de novo genome assembler for long uncorrected reads.' + edam-operations: + - term: De-novo assembly + url: http://edamontology.org/operation_0524 + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: Read pre-processing + url: http://edamontology.org/operation_3219 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Whole genome sequencing + url: http://edamontology.org/topic_3673 + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: - description: 'Raven: De novo assembly of Oxford Nanopore Technologies data' - title: Raven 1.8.0+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fraven%2Fraven%2F1.8.0%2Bgalaxy0 + title: Raven 1.8.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fraven%2Fraven%2F1.8.3%2Bgalaxy0 homepage: https://github.com/lbcb-sci/raven id: raven license: MIT @@ -15306,17 +18572,22 @@ publications: - title: 10.1101/2020.08.07.242461 url: https://doi.org/10.1101/2020.08.07.242461 - registry-link: raven - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - Whole genome sequencing - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: rawtools + biotools: rawtools bunya: '' description: A standalone tool for extracting data directly from raw files generated by Thermo Orbitrap family instruments. + edam-operations: + - term: Parsing + url: http://edamontology.org/operation_1812 + edam-topics: + - term: Proteomics experiment + url: http://edamontology.org/topic_3520 + - term: Proteomics + url: http://edamontology.org/topic_0121 galaxy: - description: 'Raw Tools: Perform scan data parsing, quantification and quality control analysis of Thermo Orbitrap raw mass spectrometer files.' @@ -15333,16 +18604,24 @@ - title: 'RawTools: Rapid and Dynamic Interrogation of Orbitrap Data Files for Mass Spectrometer System Management' url: https://doi.org/10.1021/acs.jproteome.8b00721 - registry-link: rawtools - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics experiment - - Proteomics + resources: + - title: .nan + url: .nan - biocontainers: raxml + biotools: raxml bunya: - 8.2.12 description: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. + edam-operations: + - term: Sequence analysis + url: http://edamontology.org/operation_2403 + - term: Phylogenetic tree analysis + url: http://edamontology.org/operation_0324 + edam-topics: + - term: Phylogenetics + url: http://edamontology.org/topic_3293 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'RAxML: Maximum Likelihood based inference of large phylogenetic trees' @@ -15360,16 +18639,28 @@ url: https://doi.org/10.1093/bioinformatics/btu033 - title: 10.1093/bioinformatics/btl446 url: https://doi.org/10.1093/bioinformatics/btl446 - registry-link: raxml - resource-description: .nan - resource-documentation: .nan - topics: - - Phylogenetics - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: RDKit + biotools: RDKit bunya: '' description: RDKit is an Open-Source Cheminformatics Software. Fast, Efficient Fragment-Based Coordinate Generation for Open Babel. + edam-operations: + - term: Nucleic acid structure prediction + url: http://edamontology.org/operation_0475 + - term: Molecular dynamics + url: http://edamontology.org/operation_2476 + - term: Protein geometry validation + url: http://edamontology.org/operation_1844 + edam-topics: + - term: Cheminformatics + url: http://edamontology.org/topic_2258 + - term: Medicinal chemistry + url: http://edamontology.org/topic_0209 + - term: Molecular biology + url: http://edamontology.org/topic_3047 galaxy: - description: 'Enumerate changes: calculated with Dimorphite DL and RDKit' title: Enumerate changes 2020.03.4+galaxy0 @@ -15388,16 +18679,15 @@ publications: - title: 10.26434/CHEMRXIV.7791947.V2 url: https://doi.org/10.26434/CHEMRXIV.7791947.V2 - registry-link: RDKit - resource-description: .nan - resource-documentation: .nan - topics: - - Cheminformatics - - Medicinal chemistry - - Molecular biology + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Create Frankenstein ligand: for docking active site definition' title: Create Frankenstein ligand 2013.1-0+galaxy0 @@ -15410,14 +18700,30 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: recon + biotools: recon bunya: '' description: Tool for calculating the probability of nucleosome formation along a DNA sequence input by the user. + edam-operations: + - term: Nucleosome formation or exclusion sequence prediction + url: http://edamontology.org/operation_0432 + - term: Formatting + url: http://edamontology.org/operation_0335 + edam-topics: + - term: DNA + url: http://edamontology.org/topic_0654 + - term: DNA binding sites + url: http://edamontology.org/topic_3125 + - term: Statistics and probability + url: http://edamontology.org/topic_2269 + - term: DNA packaging + url: http://edamontology.org/topic_3176 + - term: Transcription factors and regulatory sites + url: http://edamontology.org/topic_0749 galaxy: '' homepage: http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/ id: recon @@ -15430,21 +18736,30 @@ publications: - title: 'RECON: A program for prediction of nucleosome formation potential' url: http://www.ncbi.nlm.nih.gov/pubmed/15215408 - registry-link: recon - resource-description: .nan - resource-documentation: .nan - topics: - - DNA - - DNA binding sites - - Statistics and probability - - DNA packaging - - Transcription factors and regulatory sites + resources: + - title: .nan + url: .nan - biocontainers: recetox-aplcms + biotools: recetox-aplcms bunya: '' description: recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. + edam-operations: + - term: Chromatographic alignment + url: http://edamontology.org/operation_3628 + - term: Quantification + url: http://edamontology.org/operation_3799 + - term: Peak detection + url: http://edamontology.org/operation_3215 + - term: Feature extraction + url: http://edamontology.org/operation_3937 + - term: Alignment + url: http://edamontology.org/operation_2928 + edam-topics: + - term: Metabolomics + url: http://edamontology.org/topic_3172 galaxy: - description: 'recetox-aplcms - align features: align peaks across samples' title: recetox-aplcms - align features 0.12.0+galaxy1 @@ -15485,15 +18800,24 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: recetox-aplcms - resource-description: .nan - resource-documentation: .nan - topics: - - Metabolomics + resources: + - title: .nan + url: .nan - biocontainers: red + biotools: red bunya: '' description: This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data. + edam-operations: + - term: RNA-Seq analysis + url: http://edamontology.org/operation_3680 + edam-topics: + - term: RNA + url: http://edamontology.org/topic_0099 + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Data visualisation + url: http://edamontology.org/topic_0092 galaxy: - description: 'Red: repeat masking' title: Red 2018.09.10+galaxy1 @@ -15509,17 +18833,16 @@ - title: 'RED: A Java-MySQL software for identifying and visualizing RNA editing sites using rule- based and statistical filters' url: http://www.ncbi.nlm.nih.gov/pubmed/26930599 - registry-link: red - resource-description: .nan - resource-documentation: .nan - topics: - - RNA - - Sequencing - - Data visualisation + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 3.2.9 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://rgcgithub.github.io/regenie/ id: regenie @@ -15529,11 +18852,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: repeatmasker + biotools: repeatmasker bunya: - 4.1.5--pl5321hdfd78af_0 description: 'A program that screens DNA sequences for interspersed repeats and @@ -15541,6 +18864,14 @@ of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).' + edam-operations: + - term: Genome annotation + url: http://edamontology.org/operation_0362 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Sequence composition, complexity and repeats + url: http://edamontology.org/topic_0157 galaxy: - description: 'RepeatMasker: screen DNA sequences for interspersed repeats and low complexity regions' @@ -15556,13 +18887,11 @@ - 4.1.5 pawsey: '' publications: '' - registry-link: repeatmasker - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis - - Sequence composition, complexity and repeats + resources: + - title: .nan + url: .nan - biocontainers: RepeatModeler2 + biotools: RepeatModeler2 bunya: - 2.0.4--pl5321hdfd78af_0 description: RepeatModeler is a de novo transposable element (TE) family identification @@ -15570,6 +18899,24 @@ programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: de Novo sequencing + url: http://edamontology.org/operation_3644 + - term: Genome annotation + url: http://edamontology.org/operation_0362 + edam-topics: + - term: Model organisms + url: http://edamontology.org/topic_0621 + - term: Sequence composition, complexity and repeats + url: http://edamontology.org/topic_0157 + - term: Whole genome sequencing + url: http://edamontology.org/topic_3673 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Mobile genetic elements + url: http://edamontology.org/topic_0798 galaxy: - description: 'RepeatModeler: Model repetitive DNA' title: RepeatModeler 2.0.4+galaxy1 @@ -15587,18 +18934,19 @@ publications: - title: 10.1101/856591 url: https://doi.org/10.1101/856591 - registry-link: RepeatModeler2 - resource-description: .nan - resource-documentation: .nan - topics: - - Model organisms - - Sequence composition, complexity and repeats - - Whole genome sequencing - - Sequence assembly - - Mobile genetic elements + resources: + - title: .nan + url: .nan - biocontainers: RepeatScout + biotools: RepeatScout bunya: '' description: RepeatScout is a tool to discover repetitive substrings in DNA. + edam-operations: + - term: k-mer counting + url: http://edamontology.org/operation_3472 + edam-topics: + - term: DNA + url: http://edamontology.org/topic_0654 galaxy: '' homepage: http://bix.ucsd.edu/repeatscout/ id: repeatscout @@ -15611,14 +18959,15 @@ publications: - title: 10.1093/bioinformatics/bti1018 url: https://doi.org/10.1093/bioinformatics/bti1018 - registry-link: RepeatScout - resource-description: .nan - resource-documentation: .nan - topics: - - DNA + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'RepEnrich: Repeat Element Profiling' title: RepEnrich 1.6.1 @@ -15631,13 +18980,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Replace column: by values which are defined in a convert file' title: Replace column 0.2 @@ -15650,11 +19001,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: rjags + biotools: rjags bunya: - 4-10-foss-2021a-r-4.1.0 description: 'The rjags package provides an interface from R to the JAGS library @@ -15662,6 +19013,10 @@ a sequence of dependent samples from the posterior distribution of the parameters.' + edam-operations: '' + edam-topics: + - term: Statistics and probability + url: http://edamontology.org/topic_2269 galaxy: '' homepage: https://cran.r-project.org/package=rjags id: rjags @@ -15671,18 +19026,23 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: rjags - resource-description: .nan - resource-documentation: .nan - topics: - - Statistics and probability + resources: + - title: .nan + url: .nan - biocontainers: rmassbank + biotools: rmassbank bunya: '' description: Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records. + edam-operations: + - term: Clustering + url: http://edamontology.org/operation_3432 + edam-topics: + - term: Metabolomics + url: http://edamontology.org/topic_3172 galaxy: - description: 'RMassBank: ' title: RMassBank 3.0.0+galaxy2 @@ -15698,15 +19058,16 @@ - title: Automatic recalibration and processing of tandem mass spectra using formula annotation url: https://doi.org/10.1002/jms.3131 - registry-link: rmassbank - resource-description: .nan - resource-documentation: .nan - topics: - - Metabolomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 4.1.2 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: rmats-turbo @@ -15716,15 +19077,21 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: rmblast + biotools: rmblast bunya: '' description: RMBlast is a RepeatMasker compatible version of the standard NCBI blastn program. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler. + edam-operations: + - term: Sequence analysis + url: http://edamontology.org/operation_2403 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: '' homepage: http://www.repeatmasker.org/RMBlast.html id: rmblast @@ -15736,14 +19103,15 @@ - 2.14.0 pawsey: '' publications: '' - registry-link: rmblast - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Analyse canonical genes against ''peak'' data: using RnaChipIntegrator' title: Analyse canonical genes against 'peak' data 1.1.0.0 @@ -15760,15 +19128,25 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: roary + biotools: roary bunya: '' description: A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + edam-topics: + - term: DNA + url: http://edamontology.org/topic_0654 + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Mapping + url: http://edamontology.org/topic_0102 galaxy: - description: 'Roary: the pangenome pipeline - Quickly generate a core gene alignment from gff3 files' @@ -15784,16 +19162,15 @@ publications: - title: 10.1093/bioinformatics/btv421 url: https://doi.org/10.1093/bioinformatics/btv421 - registry-link: roary - resource-description: .nan - resource-documentation: .nan - topics: - - DNA - - Genomics - - Mapping + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Row Means: Calculates the mean of a row of numbers for an entire table' @@ -15807,11 +19184,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: rsem + biotools: rsem bunya: - 1.3.3--pl5321ha04fe3b_5 description: We present a generative statistical model and associated inference @@ -15820,6 +19197,12 @@ previous methods. Our improved accuracy is the result of handling read mapping uncertainty with a statistical model and the estimation of gene expression levels as the sum of isoform expression levels. + edam-operations: + - term: RNA-Seq quantification + url: http://edamontology.org/operation_3800 + edam-topics: + - term: RNA-Seq + url: http://edamontology.org/topic_3170 galaxy: '' homepage: http://deweylab.github.io/RSEM/ id: rsem @@ -15831,18 +19214,23 @@ publications: - title: RNA-Seq gene expression estimation with read mapping uncertainty url: http://www.ncbi.nlm.nih.gov/pubmed/20022975 - registry-link: rsem - resource-description: .nan - resource-documentation: .nan - topics: - - RNA-Seq + resources: + - title: .nan + url: .nan - biocontainers: rseqc + biotools: rseqc bunya: '' description: Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + edam-topics: + - term: Sequencing + url: http://edamontology.org/topic_3168 galaxy: - description: 'Gene Body Coverage (Bigwig): read coverage over gene body' title: Gene Body Coverage (Bigwig) 5.0.1+galaxy2 @@ -15935,17 +19323,28 @@ url: https://doi.org/10.1093/bioinformatics/bts356 - title: Measure transcript integrity using RNA-seq data url: https://doi.org/10.1186/s12859-016-0922-z - registry-link: rseqc - resource-description: .nan - resource-documentation: .nan - topics: - - Sequencing + resources: + - title: .nan + url: .nan - biocontainers: rstudio + biotools: rstudio bunya: '' description: Integrated development environment (IDE) for the R programming language. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + - term: Visualisation + url: http://edamontology.org/operation_0337 + edam-topics: + - term: Mathematics + url: http://edamontology.org/topic_3315 + - term: Data architecture, analysis and design + url: http://edamontology.org/topic_3365 + - term: Statistics and probability + url: http://edamontology.org/topic_2269 galaxy: - description: 'RStudio: ' - title: RStudio 0.2 + title: RStudio 0.3 url: https://usegalaxy.org.au/root?tool_id=interactive_tool_rstudio homepage: https://www.rstudio.com/ id: rstudio @@ -15957,17 +19356,22 @@ publications: - title: 'RSTUDIO: A platform-independent IDE for R and sweave' url: https://doi.org/10.1002/jae.1278 - registry-link: rstudio - resource-description: .nan - resource-documentation: .nan - topics: - - Mathematics - - Data architecture, analysis and design - - Statistics and probability + resources: + - title: .nan + url: .nan - biocontainers: rtg_core + biotools: rtg_core bunya: '' description: 'RTG Core: Software for alignment and analysis of next-gen sequencing data.' + edam-operations: + - term: Sequence alignment + url: http://edamontology.org/operation_0292 + - term: Sequence alignment analysis + url: http://edamontology.org/operation_0258 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: '' homepage: https://github.com/RealTimeGenomics/rtg-core id: rtg-tools @@ -15978,14 +19382,15 @@ - 3.12.1 pawsey: '' publications: '' - registry-link: rtg_core - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'rxDock cavity definition: - generate the active site definition needed for rxDock docking' @@ -16002,15 +19407,27 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: sailfish + biotools: sailfish bunya: '' description: A software tool that implements a novel, is an alignment-free algorithm for the estimation of isoform abundances directly from a set of reference sequences and RNA-seq reads. + edam-operations: + - term: RNA-Seq analysis + url: http://edamontology.org/operation_3680 + edam-topics: + - term: RNA-Seq + url: http://edamontology.org/topic_3170 + - term: RNA + url: http://edamontology.org/topic_0099 + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Transcriptomics + url: http://edamontology.org/topic_3308 galaxy: - description: 'Sailfish: transcript quantification from RNA-seq data' title: Sailfish 0.10.1.1 @@ -16026,19 +19443,29 @@ - title: Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms url: http://www.ncbi.nlm.nih.gov/pubmed/24752080 - registry-link: sailfish - resource-description: .nan - resource-documentation: .nan - topics: - - RNA-Seq - - RNA - - Sequencing - - Transcriptomics + resources: + - title: .nan + url: .nan - biocontainers: salmon + biotools: salmon bunya: - 1.4.0-gompi-2021a - 1.9.0-gcc-11.3.0 (D) description: A tool for transcript expression quantification from RNA-seq data + edam-operations: + - term: Sequence composition calculation + url: http://edamontology.org/operation_0236 + - term: RNA-Seq quantification + url: http://edamontology.org/operation_3800 + - term: Gene expression analysis + url: http://edamontology.org/operation_2495 + edam-topics: + - term: RNA-Seq + url: http://edamontology.org/topic_3170 + - term: Gene expression + url: http://edamontology.org/topic_0203 + - term: Transcriptomics + url: http://edamontology.org/topic_3308 galaxy: - description: 'Salmon quant: Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads' @@ -16055,16 +19482,15 @@ publications: - title: Salmon provides fast and bias-aware quantification of transcript expression url: https://doi.org/10.1038/nmeth.4197 - registry-link: salmon - resource-description: .nan - resource-documentation: .nan - topics: - - RNA-Seq - - Gene expression - - Transcriptomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'salmonKallistoMtxTo10x: Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data' @@ -16078,11 +19504,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: SALSA + biotools: SALSA bunya: - '2.3' description: '> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE ''chromosome-scale'', @@ -16092,6 +19518,20 @@ with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch' + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: De-novo assembly + url: http://edamontology.org/operation_0524 + - term: Scaffolding + url: http://edamontology.org/operation_3216 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: DNA binding sites + url: http://edamontology.org/topic_3125 + - term: Mapping + url: http://edamontology.org/topic_0102 galaxy: - description: 'SALSA: scaffold long read assemblies with Hi-C' title: SALSA 2.3+galaxy3 @@ -16106,16 +19546,15 @@ publications: - title: Integrating Hi-C links with assembly graphs for chromosome-scale assembly url: https://doi.org/10.1371/JOURNAL.PCBI.1007273 - registry-link: SALSA - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - DNA binding sites - - Mapping + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Filter SAM: on bitwise flag values' title: Filter SAM 1.0.0 @@ -16128,13 +19567,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Generate pileup: from BAM dataset' title: Generate pileup 1.1.3 @@ -16147,13 +19588,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Convert SAM: to interval' title: Convert SAM 1.0.2 @@ -16166,14 +19609,26 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: sambamba + biotools: sambamba bunya: '' description: This tool is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM, BAM and CRAM formats. + edam-operations: + - term: Sequence analysis + url: http://edamontology.org/operation_2403 + - term: Sequence alignment + url: http://edamontology.org/operation_0292 + edam-topics: + - term: DNA + url: http://edamontology.org/topic_0654 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: RNA-Seq + url: http://edamontology.org/topic_3170 galaxy: - description: 'Sample, Slice or Filter BAM: on flags, fields, and tags using Sambamba' title: Sample, Slice or Filter BAM 0.7.1+galaxy1 @@ -16190,17 +19645,24 @@ publications: - title: 'Sambamba: Fast processing of NGS alignment formats' url: http://www.ncbi.nlm.nih.gov/pubmed/25697820 - registry-link: sambamba - resource-description: .nan - resource-documentation: .nan - topics: - - DNA - - Sequence analysis - - RNA-Seq + resources: + - title: .nan + url: .nan - biocontainers: samblaster + biotools: samblaster bunya: '' description: A tool to mark duplicates and extract discordant and split reads from SAM files. + edam-operations: + - term: Split read mapping + url: http://edamontology.org/operation_3199 + edam-topics: + - term: DNA + url: http://edamontology.org/topic_0654 + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Mapping + url: http://edamontology.org/topic_0102 galaxy: '' homepage: https://github.com/GregoryFaust/samblaster id: samblaster @@ -16213,16 +19675,15 @@ publications: - title: 'SAMBLASTER: Fast duplicate marking and structural variant read extraction' url: http://www.ncbi.nlm.nih.gov/pubmed/24812344 - registry-link: samblaster - resource-description: .nan - resource-documentation: .nan - topics: - - DNA - - Sequencing - - Mapping + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Sub-sample sequences files: e.g. to reduce coverage' title: Sub-sample sequences files 0.2.5 @@ -16235,11 +19696,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: samtools + biotools: samtools bunya: - 1.13-gcc-10.3.0 - 1.13-gcc-11.3.0 @@ -16248,6 +19709,30 @@ high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. + edam-operations: + - term: Indexing + url: http://edamontology.org/operation_0227 + - term: Editing + url: http://edamontology.org/operation_3096 + - term: Parsing + url: http://edamontology.org/operation_1812 + - term: Visualisation + url: http://edamontology.org/operation_0337 + - term: Formatting + url: http://edamontology.org/operation_0335 + - term: Sorting + url: http://edamontology.org/operation_3802 + - term: Filtering + url: http://edamontology.org/operation_3695 + edam-topics: + - term: Mapping + url: http://edamontology.org/topic_0102 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Rare diseases + url: http://edamontology.org/topic_3325 galaxy: - description: 'Samtools split: BAM dataset on readgroups' title: Samtools split 1.15.1+galaxy2 @@ -16320,6 +19805,7 @@ - '1.12' nci-if89: - '1.18' + - 1.19.2 pawsey: - 1.15--h3843a85_0 publications: @@ -16330,126 +19816,132 @@ - title: A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data url: https://doi.org/10.1093/bioinformatics/btr509 - registry-link: samtools - resource-description: .nan - resource-documentation: .nan - topics: - - Mapping - - Sequence analysis - - Sequencing - - Rare diseases + resources: + - title: .nan + url: .nan - biocontainers: scanpy + biotools: scanpy bunya: '' description: Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. + edam-operations: + - term: Differential gene expression analysis + url: http://edamontology.org/operation_3223 + edam-topics: + - term: Gene expression + url: http://edamontology.org/topic_0203 + - term: Cell biology + url: http://edamontology.org/topic_2229 + - term: Genetics + url: http://edamontology.org/topic_3053 galaxy: - - description: 'Inspect and manipulate: with scanpy' - title: Inspect and manipulate 1.9.6+galaxy2 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_inspect%2Fscanpy_inspect%2F1.9.6%2Bgalaxy2 - - description: 'AnnData Operations: modifies metadata and flags genes' - title: AnnData Operations 1.8.1+galaxy93 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fanndata_ops%2Fanndata_ops%2F1.8.1%2Bgalaxy93 - description: 'Remove confounders: with scanpy' - title: Remove confounders 1.9.6+galaxy2 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_remove_confounders%2Fscanpy_remove_confounders%2F1.9.6%2Bgalaxy2 + title: Remove confounders 1.9.6+galaxy3 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_remove_confounders%2Fscanpy_remove_confounders%2F1.9.6%2Bgalaxy3 - description: 'Plot: with scanpy' - title: Plot 1.9.6+galaxy2 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_plot%2Fscanpy_plot%2F1.9.6%2Bgalaxy2 - - description: 'Normalize: and impute with scanpy' - title: Normalize 1.9.6+galaxy2 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_normalize%2Fscanpy_normalize%2F1.9.6%2Bgalaxy2 + title: Plot 1.9.6+galaxy3 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_plot%2Fscanpy_plot%2F1.9.6%2Bgalaxy3 + - description: 'Inspect and manipulate: with scanpy' + title: Inspect and manipulate 1.9.6+galaxy3 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_inspect%2Fscanpy_inspect%2F1.9.6%2Bgalaxy3 - description: 'Cluster, infer trajectories and embed: with scanpy' - title: Cluster, infer trajectories and embed 1.9.6+galaxy2 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_cluster_reduce_dimension%2Fscanpy_cluster_reduce_dimension%2F1.9.6%2Bgalaxy2 + title: Cluster, infer trajectories and embed 1.9.6+galaxy3 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_cluster_reduce_dimension%2Fscanpy_cluster_reduce_dimension%2F1.9.6%2Bgalaxy3 - description: 'Filter: with scanpy' - title: Filter 1.9.6+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_filter%2Fscanpy_filter%2F1.9.6%2Bgalaxy1 + title: Filter 1.9.6+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_filter%2Fscanpy_filter%2F1.9.6%2Bgalaxy2 - description: 'AnnData Operations: modifies metadata and flags genes' - title: AnnData Operations 1.8.1+1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fanndata_ops%2Fanndata_ops%2F1.8.1%2B1%2Bgalaxy1 - - description: 'Scanpy ComputeGraph: to derive kNN graph' - title: Scanpy ComputeGraph 1.8.1+1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_compute_graph%2Fscanpy_compute_graph%2F1.8.1%2B1%2Bgalaxy1 - - description: 'Scanpy FilterCells: based on counts and numbers of genes expressed' - title: Scanpy FilterCells 1.8.1+1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_filter_cells%2Fscanpy_filter_cells%2F1.8.1%2B1%2Bgalaxy0 + title: AnnData Operations 1.8.1+galaxy93 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fanndata_ops%2Fanndata_ops%2F1.8.1%2Bgalaxy93 + - description: 'Normalize: and impute with scanpy' + title: Normalize 1.9.6+galaxy3 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fscanpy_normalize%2Fscanpy_normalize%2F1.9.6%2Bgalaxy3 - description: 'Scanpy FilterGenes: based on counts and numbers of cells expressed' - title: Scanpy FilterGenes 1.8.1+1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_filter_genes%2Fscanpy_filter_genes%2F1.8.1%2B1%2Bgalaxy0 - - description: 'Scanpy FindCluster: based on community detection on KNN graph' - title: Scanpy FindCluster 1.8.1+1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_find_cluster%2Fscanpy_find_cluster%2F1.8.1%2B1%2Bgalaxy0 + title: Scanpy FilterGenes 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_filter_genes%2Fscanpy_filter_genes%2F1.9.3%2Bgalaxy0 + - description: 'Scanpy ScaleData: to make expression variance the same for all genes' + title: Scanpy ScaleData 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_scale_data%2Fscanpy_scale_data%2F1.9.3%2Bgalaxy0 + - description: 'Scanpy RunUMAP: visualise cell clusters using UMAP' + title: Scanpy RunUMAP 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_umap%2Fscanpy_run_umap%2F1.9.3%2Bgalaxy0 + - description: 'Scanpy RunTSNE: visualise cell clusters using tSNE' + title: Scanpy RunTSNE 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_tsne%2Fscanpy_run_tsne%2F1.9.3%2Bgalaxy0 + - description: 'Scanpy RunPCA: for dimensionality reduction' + title: Scanpy RunPCA 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_pca%2Fscanpy_run_pca%2F1.9.3%2Bgalaxy0 + - description: 'Scanpy PAGA: trajectory inference' + title: Scanpy PAGA 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_paga%2Fscanpy_run_paga%2F1.9.3%2Bgalaxy0 + - description: 'Scanpy RunFDG: visualise cell clusters using force-directed graph' + title: Scanpy RunFDG 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_fdg%2Fscanpy_run_fdg%2F1.9.3%2Bgalaxy0 + - description: 'Scanpy DPT: diffusion pseudotime inference' + title: Scanpy DPT 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_dpt%2Fscanpy_run_dpt%2F1.9.3%2Bgalaxy0 + - description: 'Scanpy DiffusionMap: calculate diffusion components' + title: Scanpy DiffusionMap 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_diffmap%2Fscanpy_run_diffmap%2F1.9.3%2Bgalaxy0 + - description: 'Scanpy Read10x: into hdf5 object handled by scanpy' + title: Scanpy Read10x 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_read_10x%2Fscanpy_read_10x%2F1.9.3%2Bgalaxy0 + - description: 'Scanpy PlotTrajectory: visualise cell trajectories' + title: Scanpy PlotTrajectory 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_plot_trajectory%2Fscanpy_plot_trajectory%2F1.9.3%2Bgalaxy0 + - description: 'Scanpy PlotEmbed: visualise cell embeddings' + title: Scanpy PlotEmbed 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_plot_embed%2Fscanpy_plot_embed%2F1.9.3%2Bgalaxy0 + - description: 'Scanpy ParameterIterator: produce an iteration over a defined parameter' + title: Scanpy ParameterIterator 0.0.1+galaxy9 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_parameter_iterator%2Fscanpy_parameter_iterator%2F0.0.1%2Bgalaxy9 + - description: 'Scanpy NormaliseData: to make all cells having the same total expression' + title: Scanpy NormaliseData 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_normalise_data%2Fscanpy_normalise_data%2F1.9.3%2Bgalaxy0 + - description: 'Scanpy MNN: correct batch effects by matching mutual nearest neighbors' + title: Scanpy MNN 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_integrate_mnn%2Fscanpy_integrate_mnn%2F1.9.3%2Bgalaxy0 + - description: 'Scanpy ComBat: adjust expression for variables that might introduce + batch effect' + title: Scanpy ComBat 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_integrate_combat%2Fscanpy_integrate_combat%2F1.9.3%2Bgalaxy0 + - description: 'Scanpy FindVariableGenes: based on normalised dispersion of expression' + title: Scanpy FindVariableGenes 1.9.3+galaxy1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_find_variable_genes%2Fscanpy_find_variable_genes%2F1.9.3%2Bgalaxy1 - description: 'Scanpy FindMarkers: to find differentially expressed genes between groups' - title: Scanpy FindMarkers 1.8.1+1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_find_markers%2Fscanpy_find_markers%2F1.8.1%2B1%2Bgalaxy0 - - description: 'Scanpy FindVariableGenes: based on normalised dispersion of expression' - title: Scanpy FindVariableGenes 1.8.1+1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_find_variable_genes%2Fscanpy_find_variable_genes%2F1.8.1%2B1%2Bgalaxy1 + title: Scanpy FindMarkers 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_find_markers%2Fscanpy_find_markers%2F1.9.3%2Bgalaxy0 + - description: 'Scanpy FindCluster: based on community detection on KNN graph' + title: Scanpy FindCluster 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_find_cluster%2Fscanpy_find_cluster%2F1.9.3%2Bgalaxy0 + - description: 'Scanpy FilterCells: based on counts and numbers of genes expressed' + title: Scanpy FilterCells 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_filter_cells%2Fscanpy_filter_cells%2F1.9.3%2Bgalaxy0 + - description: 'AnnData Operations: is a Swiss army knife for AnnData files' + title: AnnData Operations 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fanndata_ops%2Fanndata_ops%2F1.9.3%2Bgalaxy0 + - description: 'Scanpy ComputeGraph: to derive kNN graph' + title: Scanpy ComputeGraph 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_compute_graph%2Fscanpy_compute_graph%2F1.9.3%2Bgalaxy0 - description: 'Scanpy BBKNN: batch-balanced K-nearest neighbours' - title: Scanpy BBKNN 1.8.1+1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_integrate_bbknn%2Fscanpy_integrate_bbknn%2F1.8.1%2B1%2Bgalaxy0 - - description: 'Scanpy ComBat: adjust expression for variables that might introduce - batch effect' - title: Scanpy ComBat 1.8.1+1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_integrate_combat%2Fscanpy_integrate_combat%2F1.8.1%2B1%2Bgalaxy0 + title: Scanpy BBKNN 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_integrate_bbknn%2Fscanpy_integrate_bbknn%2F1.9.3%2Bgalaxy0 - description: 'Scanpy Harmony: adjust principal components for variables that might introduce batch effect' - title: Scanpy Harmony 1.8.1+1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_integrate_harmony%2Fscanpy_integrate_harmony%2F1.8.1%2B1%2Bgalaxy0 - - description: 'Scanpy MNN: correct batch effects by matching mutual nearest neighbors' - title: Scanpy MNN 1.8.1+3+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_integrate_mnn%2Fscanpy_integrate_mnn%2F1.8.1%2B3%2Bgalaxy0 + title: Scanpy Harmony 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_integrate_harmony%2Fscanpy_integrate_harmony%2F1.9.3%2Bgalaxy0 - description: 'Scanpy Scrublet: remove multiplets from annData objects with Scrublet' - title: Scanpy Scrublet 1.8.1+1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_multiplet_scrublet%2Fscanpy_multiplet_scrublet%2F1.8.1%2B1%2Bgalaxy0 - - description: 'Scanpy NormaliseData: to make all cells having the same total expression' - title: Scanpy NormaliseData 1.8.1+1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_normalise_data%2Fscanpy_normalise_data%2F1.8.1%2B1%2Bgalaxy0 - - description: 'Scanpy ParameterIterator: produce an iteration over a defined parameter' - title: Scanpy ParameterIterator 0.0.1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_parameter_iterator%2Fscanpy_parameter_iterator%2F0.0.1%2Bgalaxy0 - - description: 'Scanpy PlotEmbed: visualise cell embeddings' - title: Scanpy PlotEmbed 1.8.1+1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_plot_embed%2Fscanpy_plot_embed%2F1.8.1%2B1%2Bgalaxy0 + title: Scanpy Scrublet 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_multiplet_scrublet%2Fscanpy_multiplet_scrublet%2F1.9.3%2Bgalaxy0 - description: 'Scanpy Plot Scrublet: visualise multiplet scoring distribution' - title: Scanpy Plot Scrublet 1.8.1+1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_plot_scrublet%2Fscanpy_plot_scrublet%2F1.8.1%2B1%2Bgalaxy0 - - description: 'Scanpy PlotTrajectory: visualise cell trajectories' - title: Scanpy PlotTrajectory 1.8.1+1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_plot_trajectory%2Fscanpy_plot_trajectory%2F1.8.1%2B1%2Bgalaxy0 - - description: 'Scanpy Read10x: into hdf5 object handled by scanpy' - title: Scanpy Read10x 1.8.1+1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_read_10x%2Fscanpy_read_10x%2F1.8.1%2B1%2Bgalaxy0 + title: Scanpy Plot Scrublet 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_plot_scrublet%2Fscanpy_plot_scrublet%2F1.9.3%2Bgalaxy0 - description: 'Scanpy RegressOut: variables that might introduce batch effect' - title: Scanpy RegressOut 1.8.1+1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_regress_variable%2Fscanpy_regress_variable%2F1.8.1%2B1%2Bgalaxy0 - - description: 'Scanpy DiffusionMap: calculate diffusion components' - title: Scanpy DiffusionMap 1.8.1+1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_diffmap%2Fscanpy_run_diffmap%2F1.8.1%2B1%2Bgalaxy0 - - description: 'Scanpy DPT: diffusion pseudotime inference' - title: Scanpy DPT 1.8.1+1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_dpt%2Fscanpy_run_dpt%2F1.8.1%2B1%2Bgalaxy0 - - description: 'Scanpy RunFDG: visualise cell clusters using force-directed graph' - title: Scanpy RunFDG 1.8.1+1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_fdg%2Fscanpy_run_fdg%2F1.8.1%2B1%2Bgalaxy0 - - description: 'Scanpy PAGA: trajectory inference' - title: Scanpy PAGA 1.8.1+1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_paga%2Fscanpy_run_paga%2F1.8.1%2B1%2Bgalaxy0 - - description: 'Scanpy RunPCA: for dimensionality reduction' - title: Scanpy RunPCA 1.8.1+1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_pca%2Fscanpy_run_pca%2F1.8.1%2B1%2Bgalaxy0 - - description: 'Scanpy RunTSNE: visualise cell clusters using tSNE' - title: Scanpy RunTSNE 1.8.1+1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_tsne%2Fscanpy_run_tsne%2F1.8.1%2B1%2Bgalaxy1 - - description: 'Scanpy RunUMAP: visualise cell clusters using UMAP' - title: Scanpy RunUMAP 1.8.1+3+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_run_umap%2Fscanpy_run_umap%2F1.8.1%2B3%2Bgalaxy0 - - description: 'Scanpy ScaleData: to make expression variance the same for all genes' - title: Scanpy ScaleData 1.8.1+1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_scale_data%2Fscanpy_scale_data%2F1.8.1%2B1%2Bgalaxy0 + title: Scanpy RegressOut 1.9.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fscanpy_regress_variable%2Fscanpy_regress_variable%2F1.9.3%2Bgalaxy0 homepage: https://github.com/theislab/Scanpy id: scanpy license: BSD-3-Clause @@ -16460,17 +19952,28 @@ publications: - title: 'SCANPY: Large-scale single-cell gene expression data analysis' url: https://doi.org/10.1186/s13059-017-1382-0 - registry-link: scanpy - resource-description: .nan - resource-documentation: .nan - topics: - - Gene expression - - Cell biology - - Genetics + resources: + - title: .nan + url: .nan - biocontainers: scater + biotools: scater bunya: '' description: Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. + edam-operations: + - term: Read pre-processing + url: http://edamontology.org/operation_3219 + - term: Sequencing quality control + url: http://edamontology.org/operation_3218 + - term: Sequence visualisation + url: http://edamontology.org/operation_0564 + edam-topics: + - term: RNA-seq + url: http://edamontology.org/topic_3170 + - term: Quality affairs + url: http://edamontology.org/topic_3393 + - term: Molecular genetics + url: http://edamontology.org/topic_3321 galaxy: - description: 'Scater: t-SNE plot: of two components' title: 'Scater: t-SNE plot 1.22.0' @@ -16503,17 +20006,16 @@ - title: 'Scater: Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R' url: https://doi.org/10.1093/bioinformatics/btw777 - registry-link: scater - resource-description: .nan - resource-documentation: .nan - topics: - - RNA-seq - - Quality affairs - - Molecular genetics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 0.11.1-gcccore-10.3.0 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: scikit-build @@ -16523,24 +20025,40 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: scikit-image + biotools: scikit-image bunya: '' description: Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. - galaxy: + edam-operations: + - term: Image analysis + url: http://edamontology.org/operation_3443 + - term: Image annotation + url: http://edamontology.org/operation_3553 + - term: Visualisation + url: http://edamontology.org/operation_0337 + - term: Data handling + url: http://edamontology.org/operation_2409 + edam-topics: + - term: Imaging + url: http://edamontology.org/topic_3382 + - term: Software engineering + url: http://edamontology.org/topic_3372 + - term: Literature and language + url: http://edamontology.org/topic_3068 + galaxy: + - description: 'Extract image features: with scikit-image' + title: Extract image features 0.18.1+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2F2d_feature_extraction%2Fip_2d_feature_extraction%2F0.18.1%2Bgalaxy0 - description: 'Count objects in label map: ' title: Count objects in label map 0.0.5-2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2Fcount_objects%2Fip_count_objects%2F0.0.5-2 - description: 'Threshold image: with scikit-image' title: Threshold image 0.18.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2F2d_auto_threshold%2Fip_threshold%2F0.18.1%2Bgalaxy1 - - description: 'Extract 2D features: with scikit-image' - title: Extract 2D features 0.1.1-2 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2F2d_feature_extraction%2Fip_2d_feature_extraction%2F0.1.1-2 - description: 'Filter label map by rules: ' title: Filter label map by rules 0.0.1-2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2F2d_filter_segmentation_by_features%2Fip_2d_filter_segmentation_by_features%2F0.0.1-2 @@ -16563,16 +20081,15 @@ publications: - title: 10.7287/PEERJ.PREPRINTS.336V2 url: https://doi.org/10.7287/PEERJ.PREPRINTS.336V2 - registry-link: scikit-image - resource-description: .nan - resource-documentation: .nan - topics: - - Imaging - - Software engineering - - Literature and language + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Estimator attributes: get important attributes from an estimator or scikit object' @@ -16631,13 +20148,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://www.webscipio.org/ id: scipio @@ -16648,13 +20167,15 @@ - '1.4' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Extract values from an SD-file: into a tabular file using RDKit' title: Extract values from an SD-file 2020.03.4+galaxy0 @@ -16667,13 +20188,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Send to cloud: ' title: Send to cloud 0.1.0 @@ -16686,16 +20209,22 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: sepp + biotools: sepp bunya: - 4.5.0-foss-2021a - 4.5.1-foss-2022a (D) description: "SEPP stands for SAT\xE9-Enabled Phylogenetic Placement and addresses\ \ the problem of phylogenetic placement for meta-genomic short reads" + edam-operations: + - term: Phylogenetic analysis + url: http://edamontology.org/operation_0324 + edam-topics: + - term: Phylogenetics + url: http://edamontology.org/topic_3293 galaxy: '' homepage: https://github.com/smirarab/sepp id: sepp @@ -16708,14 +20237,15 @@ publications: - title: 10.1142/9789814366496_0024 url: https://doi.org/10.1142/9789814366496_0024 - registry-link: sepp - resource-description: .nan - resource-documentation: .nan - topics: - - Phylogenetics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Filter sequences by ID: from a tabular file' title: Filter sequences by ID 0.2.9 @@ -16728,13 +20258,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Select sequences by ID: from a tabular file' title: Select sequences by ID 0.0.14 @@ -16747,11 +20279,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: seqkit + biotools: seqkit bunya: '' description: FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, @@ -16763,7 +20295,27 @@ in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. - galaxy: '' + edam-operations: + - term: DNA transcription + url: http://edamontology.org/operation_0372 + - term: Sequence trimming + url: http://edamontology.org/operation_3192 + - term: DNA translation + url: http://edamontology.org/operation_0371 + - term: Sequence conversion + url: http://edamontology.org/operation_0233 + edam-topics: + - term: Database management + url: http://edamontology.org/topic_3489 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + galaxy: + - description: 'SeqKit statistics: of FASTA/Q files' + title: SeqKit statistics 2.8.1+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseqkit_stats%2Fseqkit_stats%2F2.8.1%2Bgalaxy0 + - description: 'SeqKit sort: FASTA or FASTQ files' + title: SeqKit sort 2.3.1+galaxy1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseqkit_sort%2Fseqkit_sort%2F2.3.1%2Bgalaxy1 homepage: https://bioinf.shenwei.me/seqkit/ id: seqkit license: '' @@ -16772,20 +20324,21 @@ nci-if89: - 2.2.0 - 2.3.1 + - 2.5.1 pawsey: '' publications: - title: 10.1371/journal.pone.0163962 url: https://doi.org/10.1371/journal.pone.0163962 - registry-link: seqkit - resource-description: .nan - resource-documentation: .nan - topics: - - Database management - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 1.2.0-gcc-10.3.0 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: seqlib @@ -16795,16 +20348,24 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: seqtk + biotools: seqtk bunya: - 1.3-gcc-10.3.0 - 1.3-gcc-11.3.0 (D) description: A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + - term: Sequence file editing + url: http://edamontology.org/operation_2121 + edam-topics: + - term: Data management + url: http://edamontology.org/topic_3071 galaxy: - description: 'seqtk_telo: find telomeres' title: seqtk_telo 1.4+galaxy0 @@ -16858,23 +20419,29 @@ name: seqtk nci-gadi: - '1.3' - nci-if89: '' + nci-if89: + - '1.4' pawsey: '' publications: - title: 'FastQ-brew: Module for analysis, preprocessing, and reformatting of FASTQ sequence data' url: https://doi.org/10.1186/s13104-017-2616-7 - registry-link: seqtk - resource-description: .nan - resource-documentation: .nan - topics: - - Data management + resources: + - title: .nan + url: .nan - biocontainers: seurat + biotools: seurat bunya: '' description: Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. + edam-operations: '' + edam-topics: + - term: RNA-Seq + url: http://edamontology.org/topic_3170 + - term: Transcriptomics + url: http://edamontology.org/topic_3308 galaxy: - description: 'Seurat: - toolkit for exploration of single-cell RNA-seq data' title: Seurat 4.3.0.1+galaxy1 @@ -16889,15 +20456,15 @@ publications: - title: Integrated analysis of multimodal single-cell data url: https://doi.org/10.1016/j.cell.2021.04.048 - registry-link: seurat - resource-description: .nan - resource-documentation: .nan - topics: - - RNA-Seq - - Transcriptomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'SFF converter: ' title: SFF converter 1.0.1 @@ -16910,13 +20477,21 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: shasta + biotools: shasta bunya: '' description: De novo assembly from Oxford Nanopore reads. + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: - description: 'Shasta: De novo assembly of long read sequencing data' title: Shasta 0.6.0+galaxy0 @@ -16932,13 +20507,11 @@ - title: Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes url: https://doi.org/10.1038/s41587-020-0503-6 - registry-link: shasta - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Sequence assembly + resources: + - title: .nan + url: .nan - biocontainers: shovill + biotools: shovill bunya: - 1.1.0 description: Shovill is a pipeline for assembly of bacterial isolate genomes from @@ -16947,6 +20520,16 @@ Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Microbiology + url: http://edamontology.org/topic_3301 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: - description: 'Shovill: Faster SPAdes assembly of Illumina reads' title: Shovill 1.1.0+galaxy2 @@ -16959,17 +20542,22 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: shovill - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Microbiology - - Sequence assembly + resources: + - title: .nan + url: .nan - biocontainers: sicer + biotools: sicer bunya: '' description: A clustering approach for identification of enriched domains from histone modification ChIP-seq data. + edam-operations: + - term: Sequence contamination filtering + url: http://edamontology.org/operation_3187 + edam-topics: + - term: ChIP-seq + url: http://edamontology.org/topic_3169 + - term: Epigenomics + url: http://edamontology.org/topic_3173 galaxy: - description: 'SICER: Statistical approach for the Identification of ChIP-Enriched Regions' @@ -16986,13 +20574,11 @@ - title: A clustering approach for identification of enriched domains from histone modification ChIP-Seq data url: http://www.ncbi.nlm.nih.gov/pubmed/19505939 - registry-link: sicer - resource-description: .nan - resource-documentation: .nan - topics: - - ChIP-seq - - Epigenomics + resources: + - title: .nan + url: .nan - biocontainers: simtext + biotools: simtext bunya: '' description: 'A text mining framework for interactive analysis and visualization of similarities among biomedical entities. @@ -17006,6 +20592,24 @@ For all PMIDs in each row of a table the according abstracts are saved in additional columns.' + edam-operations: + - term: Text mining + url: http://edamontology.org/operation_0306 + - term: Database search + url: http://edamontology.org/operation_2421 + - term: Text annotation + url: http://edamontology.org/operation_3778 + - term: Clustering + url: http://edamontology.org/operation_3432 + edam-topics: + - term: Natural language processing + url: http://edamontology.org/topic_0218 + - term: Workflows + url: http://edamontology.org/topic_0769 + - term: Machine learning + url: http://edamontology.org/topic_3474 + - term: Molecular interactions, pathways and networks + url: http://edamontology.org/topic_0602 galaxy: - description: 'PMIDs to PubTator: binary matrix' title: PMIDs to PubTator 0.0.2 @@ -17024,17 +20628,15 @@ publications: - title: 10.1101/2020.07.06.190629 url: https://doi.org/10.1101/2020.07.06.190629 - registry-link: simtext - resource-description: .nan - resource-documentation: .nan - topics: - - Natural language processing - - Workflows - - Machine learning - - Molecular interactions, pathways and networks + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: sip @@ -17045,15 +20647,33 @@ - 6.7.9 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: SISTR + biotools: SISTR bunya: '' description: The Salmonella In Silico Typing Resource (SISTR) is an open-source and freely available web application for rapid in silico typing and serovar prediction from Salmonella genome assemblies using cgMLST and O and H antigen gene searching. + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: Visualisation + url: http://edamontology.org/operation_0337 + - term: Multilocus sequence typing + url: http://edamontology.org/operation_3840 + edam-topics: + - term: Whole genome sequencing + url: http://edamontology.org/topic_3673 + - term: Immunoproteins and antigens + url: http://edamontology.org/topic_2830 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Zoology + url: http://edamontology.org/topic_3500 + - term: Public health and epidemiology + url: http://edamontology.org/topic_3305 galaxy: - description: 'sistr_cmd: Salmonella In Silico Typing Resource commandline tool for serovar prediction' @@ -17070,18 +20690,15 @@ - title: Performance and accuracy of four open-source tools for in silico serotyping of salmonella spp. Based on whole-genome short-read sequencing data url: https://doi.org/10.1128/AEM.02265-19 - registry-link: SISTR - resource-description: .nan - resource-documentation: .nan - topics: - - Whole genome sequencing - - Immunoproteins and antigens - - Sequence assembly - - Zoology - - Public health and epidemiology + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: slow5-dorado @@ -17092,13 +20709,15 @@ - 0.2.1 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: slow5-guppy @@ -17109,13 +20728,15 @@ - 6.0.1 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://github.com/hasindu2008/slow5tools id: slow5tools @@ -17126,16 +20747,19 @@ nci-if89: - 0.3.0 - 1.0.0 + - 1.1.0 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 20160702-gcccore-10.3.0 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: smithwaterman @@ -17145,11 +20769,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: Smudgeplots + biotools: Smudgeplots bunya: '' description: 'Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots @@ -17162,6 +20786,20 @@ etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568' + edam-operations: + - term: Sequence trimming + url: http://edamontology.org/operation_3192 + - term: Genotyping + url: http://edamontology.org/operation_3196 + - term: k-mer counting + url: http://edamontology.org/operation_3472 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Genetic variation + url: http://edamontology.org/topic_0199 + - term: Mathematics + url: http://edamontology.org/topic_3315 galaxy: - description: 'Smudgeplot: inference of ploidy and heterozygosity structure using whole genome sequencing' @@ -17177,14 +20815,11 @@ publications: - title: 10.1101/747568 url: https://doi.org/10.1101/747568 - registry-link: Smudgeplots - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - Genetic variation - - Mathematics + resources: + - title: .nan + url: .nan - biocontainers: snakemake + biotools: snakemake bunya: - 6.6.1-foss-2021a - 7.22.0-foss-2022a (D) @@ -17192,6 +20827,16 @@ workflows by providing a fast and comfortable execution environment, together with a clean and modern domain specific specification language (DSL) in python style. + edam-operations: + - term: Service composition + url: http://edamontology.org/operation_3762 + edam-topics: + - term: Bioinformatics + url: http://edamontology.org/topic_0091 + - term: Workflows + url: http://edamontology.org/topic_0769 + - term: Software engineering + url: http://edamontology.org/topic_3372 galaxy: '' homepage: https://snakemake.readthedocs.io/en/stable/index.html id: snakemake @@ -17204,17 +20849,24 @@ publications: - title: Snakemake-a scalable bioinformatics workflow engine url: http://www.ncbi.nlm.nih.gov/pubmed/22908215 - registry-link: snakemake - resource-description: .nan - resource-documentation: .nan - topics: - - Bioinformatics - - Workflows - - Software engineering + resources: + - title: .nan + url: .nan - biocontainers: snap + biotools: snap bunya: - '2013_11_29' description: The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. + edam-operations: + - term: Gene prediction + url: http://edamontology.org/operation_2454 + edam-topics: + - term: DNA + url: http://edamontology.org/topic_0654 + - term: DNA polymorphism + url: http://edamontology.org/topic_2885 + - term: Genetics + url: http://edamontology.org/topic_3053 galaxy: - description: 'Train SNAP: ab-initio gene predictor' title: Train SNAP 2013_11_29+galaxy1 @@ -17230,14 +20882,11 @@ publications: - title: 10.1186/1471-2105-5-59 url: https://doi.org/10.1186/1471-2105-5-59 - registry-link: snap - resource-description: .nan - resource-documentation: .nan - topics: - - DNA - - DNA polymorphism - - Genetics + resources: + - title: .nan + url: .nan - biocontainers: SNAPPy + biotools: SNAPPy bunya: - 1.1.8-gcccore-10.3.0 - 1.1.9-gcccore-11.3.0 (D) @@ -17252,6 +20901,20 @@ \ works please visit the documentation page. SNAPPy was design for Linux based\ \ operative systems | Welcome to snappy\u2019s documentation! \u2014 SNAPPy-HIV1-Subtyping\ \ 1.0.0 documentation | Free document hosting provided by Read the Docs" + edam-operations: + - term: Sequence trimming + url: http://edamontology.org/operation_3192 + - term: Parsing + url: http://edamontology.org/operation_1812 + - term: Genotyping + url: http://edamontology.org/operation_3196 + edam-topics: + - term: Phylogenetics + url: http://edamontology.org/topic_3293 + - term: Workflows + url: http://edamontology.org/topic_0769 + - term: Public health and epidemiology + url: http://edamontology.org/topic_3305 galaxy: '' homepage: https://github.com/PMMAraujo/snappy id: snappy @@ -17264,17 +20927,24 @@ - title: 'SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing' url: https://doi.org/10.1093/ve/vez050 - registry-link: SNAPPy - resource-description: .nan - resource-documentation: .nan - topics: - - Phylogenetics - - Workflows - - Public health and epidemiology + resources: + - title: .nan + url: .nan - biocontainers: sniffles + biotools: sniffles bunya: '' description: An algorithm for structural variation detection from third generation sequencing alignment. + edam-operations: + - term: Sequence analysis + url: http://edamontology.org/operation_2403 + - term: Structural variation detection + url: http://edamontology.org/operation_3228 + edam-topics: + - term: DNA structural variation + url: http://edamontology.org/topic_3175 + - term: Sequencing + url: http://edamontology.org/topic_3168 galaxy: - description: 'sniffles: Structural variation caller using third generation sequencing' title: sniffles 1.0.12+galaxy0 @@ -17291,15 +20961,29 @@ - title: Accurate detection of complex structural variations using single-molecule sequencing url: https://doi.org/10.1038/s41592-018-0001-7 - registry-link: sniffles - resource-description: .nan - resource-documentation: .nan - topics: - - DNA structural variation - - Sequencing + resources: + - title: .nan + url: .nan - biocontainers: snippy + biotools: snippy bunya: '' description: Rapid haploid variant calling and core SNP phylogeny generation. + edam-operations: + - term: Phylogenetic tree visualisation + url: http://edamontology.org/operation_0567 + - term: Phylogenetic tree generation + url: http://edamontology.org/operation_0323 + - term: Variant calling + url: http://edamontology.org/operation_3227 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Model organisms + url: http://edamontology.org/topic_0621 + - term: DNA polymorphism + url: http://edamontology.org/topic_2885 + - term: Phylogenetics + url: http://edamontology.org/topic_3293 galaxy: - description: 'snippy-clean_full_aln: Replace any non-standard sequence characters in snippy ''core.full.aln'' file.' @@ -17320,17 +21004,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: snippy - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Model organisms - - DNA polymorphism - - Phylogenetics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Finds SNP sites: from a multi-FASTA alignment file' title: Finds SNP sites 2.5.1+galaxy0 @@ -17343,13 +21025,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'SNP distance matrix: Compute distance in SNPs between all sequences in a FASTA file' @@ -17363,14 +21047,24 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: snpeff + biotools: snpeff bunya: '' description: Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). + edam-operations: + - term: SNP detection + url: http://edamontology.org/operation_0484 + edam-topics: + - term: DNA polymorphism + url: http://edamontology.org/topic_2885 + - term: Genetic variation + url: http://edamontology.org/topic_0199 + - term: Nucleic acid sites, features and motifs + url: http://edamontology.org/topic_3511 galaxy: - description: 'SnpEff chromosome-info:: list chromosome names/lengths' title: 'SnpEff chromosome-info: 4.3+T.galaxy2' @@ -17400,16 +21094,15 @@ publications: - title: '22728672' url: http://www.ncbi.nlm.nih.gov/pubmed/22728672 - registry-link: snpeff - resource-description: .nan - resource-documentation: .nan - topics: - - DNA polymorphism - - Genetic variation - - Nucleic acid sites, features and motifs + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'snpFreq: significant SNPs in case-control data' title: snpFreq 1.0.1 @@ -17422,13 +21115,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Variant Frequency Plot: Generates a heatmap of allele frequencies grouped by variant type for SnpEff-annotated SARS-CoV-2 data' @@ -17442,13 +21137,21 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: snpsift + biotools: snpsift bunya: '' description: Toolbox that allows you to filter and manipulate annotated vcf files. + edam-operations: + - term: Variant filtering + url: http://edamontology.org/operation_3675 + edam-topics: + - term: Data management + url: http://edamontology.org/topic_3071 + - term: Data architecture, analysis and design + url: http://edamontology.org/topic_3365 galaxy: - description: 'SnpSift CaseControl: Count samples are in ''case'' and ''control'' groups.' @@ -17486,15 +21189,29 @@ - title: Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift url: https://doi.org/10.3389/fgene.2012.00035 - registry-link: snpsift - resource-description: .nan - resource-documentation: .nan - topics: - - Data management - - Data architecture, analysis and design + resources: + - title: .nan + url: .nan - biocontainers: soapdenovo2 + biotools: soapdenovo2 bunya: '' description: SOAPdenovo2 is a next generation sequencing reads de novo assembler. + edam-operations: + - term: Scaffolding + url: http://edamontology.org/operation_3216 + - term: De-novo assembly + url: http://edamontology.org/operation_0524 + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: Sorting + url: http://edamontology.org/operation_3802 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Metagenomics + url: http://edamontology.org/topic_3174 galaxy: '' homepage: https://github.com/aquaskyline/SOAPdenovo2 id: soapdenovo2 @@ -17508,17 +21225,26 @@ - title: 'SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler' url: https://doi.org/10.1186/2047-217X-1-18 - registry-link: soapdenovo2 - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - Sequencing - - Metagenomics + resources: + - title: .nan + url: .nan - biocontainers: sortmerna + biotools: sortmerna bunya: - 4.3.6--h9ee0642_0 description: Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. + edam-operations: + - term: Sequence similarity search + url: http://edamontology.org/operation_0346 + - term: Sequence comparison + url: http://edamontology.org/operation_2451 + - term: Sequence alignment analysis + url: http://edamontology.org/operation_0258 + edam-topics: + - term: Metatranscriptomics + url: http://edamontology.org/topic_3941 + - term: Metagenomics + url: http://edamontology.org/topic_3174 galaxy: - description: 'Filter with SortMeRNA: of ribosomal RNAs in metatranscriptomic data' title: Filter with SortMeRNA 4.3.6+galaxy0 @@ -17534,16 +21260,16 @@ - title: 'SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data' url: https://doi.org/10.1093/bioinformatics/bts611 - registry-link: sortmerna - resource-description: .nan - resource-documentation: .nan - topics: - - Metatranscriptomics - - Metagenomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 2.0.1-gcc-11.3.0 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://www.10xgenomics.com/support/software/space-ranger/latest id: spaceranger @@ -17553,11 +21279,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: spades + biotools: spades bunya: - 3.15.3-gcc-10.3.0 - 3.15.5-gcc-11.3.0 (D) @@ -17566,35 +21292,41 @@ \ or IonTorrent reads and is capable of providing hybrid assemblies using PacBio,\ \ Oxford Nanopore and Sanger reads. Additional contigs can be provided and can\ \ be used as long reads." + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: - description: 'SPAdes: genome assembler for genomes of regular and single-cell projects' - title: SPAdes 3.15.5+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fspades%2Fspades%2F3.15.5%2Bgalaxy0 + title: SPAdes 3.15.5+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fspades%2Fspades%2F3.15.5%2Bgalaxy2 - description: 'rnaviralSPAdes: de novo assembler for transcriptomes, metatranscriptomes and metaviromes' - title: rnaviralSPAdes 3.15.5+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fspades_rnaviralspades%2Fspades_rnaviralspades%2F3.15.5%2Bgalaxy1 + title: rnaviralSPAdes 3.15.5+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fspades_rnaviralspades%2Fspades_rnaviralspades%2F3.15.5%2Bgalaxy2 - description: 'metaviralSPAdes: extract and assembly viral genomes from metagenomic data' - title: metaviralSPAdes 3.15.5+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fspades_metaviralspades%2Fspades_metaviralspades%2F3.15.5%2Bgalaxy1 + title: metaviralSPAdes 3.15.5+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fspades_metaviralspades%2Fspades_metaviralspades%2F3.15.5%2Bgalaxy2 - description: 'metaplasmidSPAdes: extract and assembly plasmids from metagenomic data' - title: metaplasmidSPAdes 3.15.5+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fspades_metaplasmidspades%2Fspades_metaplasmidspades%2F3.15.5%2Bgalaxy1 + title: metaplasmidSPAdes 3.15.5+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fspades_metaplasmidspades%2Fspades_metaplasmidspades%2F3.15.5%2Bgalaxy2 - description: 'coronaSPAdes: SARS-CoV-2 de novo genome assembler' - title: coronaSPAdes 3.15.5+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fspades_coronaspades%2Fspades_coronaspades%2F3.15.5%2Bgalaxy1 + title: coronaSPAdes 3.15.5+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fspades_coronaspades%2Fspades_coronaspades%2F3.15.5%2Bgalaxy2 - description: 'biosyntheticSPAdes: biosynthetic gene cluster assembly' - title: biosyntheticSPAdes 3.15.5+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fspades_biosyntheticspades%2Fspades_biosyntheticspades%2F3.15.5%2Bgalaxy1 + title: biosyntheticSPAdes 3.15.5+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fspades_biosyntheticspades%2Fspades_biosyntheticspades%2F3.15.5%2Bgalaxy2 - description: 'rnaSPAdes: de novo transcriptome assembler' - title: rnaSPAdes 3.15.5+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Frnaspades%2Frnaspades%2F3.15.5%2Bgalaxy1 + title: rnaSPAdes 3.15.5+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Frnaspades%2Frnaspades%2F3.15.5%2Bgalaxy2 - description: 'plasmidSPAdes: extract and assembly plasmids from WGS data' - title: plasmidSPAdes 3.15.4+galaxy2 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fspades_plasmidspades%2Fspades_plasmidspades%2F3.15.4%2Bgalaxy2 + title: plasmidSPAdes 3.15.5+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fspades_plasmidspades%2Fspades_plasmidspades%2F3.15.5%2Bgalaxy2 homepage: http://cab.spbu.ru/software/spades/ id: spades license: GPL-2.0 @@ -17609,15 +21341,16 @@ url: https://doi.org/10.1089/cmb.2012.0021 - title: 10.7490/f1000research.1114334.1 url: https://doi.org/10.7490/f1000research.1114334.1 - registry-link: spades - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 1.0.1-gcccore-11.3.0 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: spectra @@ -17627,14 +21360,20 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: srf + biotools: srf bunya: '' description: Spectral Repeat Finder (SRF) is a program to find repeats through an analysis of the power spectrum of a given DNA sequence. + edam-operations: + - term: Analysis + url: http://edamontology.org/operation_2945 + edam-topics: + - term: Computational biology + url: http://edamontology.org/topic_3307 galaxy: '' homepage: https://webs.iiitd.edu.in/raghava/srf/ id: srf @@ -17648,18 +21387,19 @@ - title: 'Spectral repeat finders (SRF): Identification of repetitive sequences using Fourier transformation' url: https://doi.org/10.1093/bioinformatics/bth103 - registry-link: srf - resource-description: .nan - resource-documentation: .nan - topics: - - Computational biology + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Split file: to dataset collection' - title: Split file 0.5.1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsplit_file_to_collection%2Fsplit_file_to_collection%2F0.5.1 + title: Split file 0.5.2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsplit_file_to_collection%2Fsplit_file_to_collection%2F0.5.2 homepage: '' id: split_file_to_collection license: '' @@ -17668,13 +21408,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://www.sqlite.org/index.html id: sqlite @@ -17685,13 +21427,15 @@ - '3.36' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'SQLite to tabular: for SQL query' title: SQLite to tabular 3.2.0 @@ -17704,13 +21448,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'SRA: server' title: SRA 1.0.1 @@ -17723,26 +21469,36 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: sra-tools + biotools: sra-tools bunya: - 3.0.3-gompi-2022a - 3.0.3--h87f3376_0 description: The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + edam-topics: + - term: DNA + url: http://edamontology.org/topic_0654 + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Sequencing + url: http://edamontology.org/topic_3168 galaxy: - description: 'Download and Extract Reads in BAM: format from NCBI SRA' - title: Download and Extract Reads in BAM 3.1.0+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Fsam_dump%2F3.1.0%2Bgalaxy0 + title: Download and Extract Reads in BAM 3.1.1+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Fsam_dump%2F3.1.1%2Bgalaxy0 - description: 'Faster Download and Extract Reads in FASTQ: format from NCBI SRA' - title: Faster Download and Extract Reads in FASTQ 3.1.0+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Ffasterq_dump%2F3.1.0%2Bgalaxy0 + title: Faster Download and Extract Reads in FASTQ 3.1.1+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Ffasterq_dump%2F3.1.1%2Bgalaxy0 - description: 'Download and Extract Reads in FASTQ: format from NCBI SRA' - title: Download and Extract Reads in FASTQ 3.1.0+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Ffastq_dump%2F3.1.0%2Bgalaxy0 + title: Download and Extract Reads in FASTQ 3.1.1+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Ffastq_dump%2F3.1.1%2Bgalaxy0 homepage: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc id: sra-tools license: '' @@ -17754,17 +21510,16 @@ publications: - title: Database resources of the National Center for Biotechnology Information. url: http://www.ncbi.nlm.nih.gov/pubmed/16381840 - registry-link: sra-tools - resource-description: .nan - resource-documentation: .nan - topics: - - DNA - - Genomics - - Sequencing + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 0.2.0--py_4 description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://github.com/katholt/srst2 id: srst2 @@ -17774,15 +21529,29 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: ssw + biotools: ssw bunya: - 1.1-gcccore-10.3.0 description: A fast implementation of the Smith-Waterman algorithm whose API that can be flexibly used by programs written in C, C++ and other languages. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + - term: Sequence alignment + url: http://edamontology.org/operation_0292 + edam-topics: + - term: Sample collections + url: http://edamontology.org/topic_3277 + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Data governance + url: http://edamontology.org/topic_3571 + - term: Nucleic acid structure analysis + url: http://edamontology.org/topic_0097 galaxy: '' homepage: http://blog.gkno.me/post/42508822069/ssw-library id: ssw @@ -17794,19 +21563,23 @@ publications: - title: 'SSW library: An SIMD Smith-Waterman C/C++ library for use in genomic applications' url: http://www.ncbi.nlm.nih.gov/pubmed/24324759 - registry-link: ssw - resource-description: .nan - resource-documentation: .nan - topics: - - Sample collections - - Genomics - - Data governance - - Nucleic acid structure analysis + resources: + - title: .nan + url: .nan - biocontainers: stacks + biotools: stacks bunya: '' description: Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + edam-topics: + - term: Mapping + url: http://edamontology.org/topic_0102 + - term: Population genetics + url: http://edamontology.org/topic_3056 galaxy: - description: 'Stacks2: clone filter: Identify PCR clones' title: 'Stacks2: clone filter 2.55+galaxy4' @@ -17902,18 +21675,24 @@ publications: - title: 'Stacks: An analysis tool set for population genomics' url: https://doi.org/10.1111/mec.12354 - registry-link: stacks - resource-description: .nan - resource-documentation: .nan - topics: - - Mapping - - Population genetics + resources: + - title: .nan + url: .nan - biocontainers: star + biotools: star bunya: - 2.7.9a-gcc-10.3.0 - 2.7.10b-gcc-11.3.0 (D) - 2.7.10a--h9ee0642_0 description: Ultrafast universal RNA-seq data aligner + edam-operations: + - term: Sequence alignment + url: http://edamontology.org/operation_0292 + edam-topics: + - term: RNA-Seq + url: http://edamontology.org/topic_3170 + - term: Transcriptomics + url: http://edamontology.org/topic_3308 galaxy: - description: 'RNA STAR: Gapped-read mapper for RNA-seq data' title: RNA STAR 2.7.11a+galaxy0 @@ -17934,15 +21713,15 @@ url: https://doi.org/10.1038/nmeth.4106 - title: Lacking alignments? The next-generation sequencing mapper segemehl revisited url: https://doi.org/10.1093/bioinformatics/btu146 - registry-link: star - resource-description: .nan - resource-documentation: .nan - topics: - - RNA-Seq - - Transcriptomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'staramr: Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.' @@ -17956,14 +21735,22 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: star-fusion + biotools: star-fusion bunya: '' description: STAR-Fusion, a method that is both fast and accurate in identifying fusion transcripts from RNA-Seq data + edam-operations: + - term: Sequence analysis + url: http://edamontology.org/operation_2403 + edam-topics: + - term: Gene structure + url: http://edamontology.org/topic_0114 + - term: RNA-Seq + url: http://edamontology.org/topic_3170 galaxy: - description: 'STAR-Fusion: detect fusion genes in RNA-Seq data' title: STAR-Fusion 0.5.4-3+galaxy1 @@ -17976,26 +21763,34 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: star-fusion - resource-description: .nan - resource-documentation: .nan - topics: - - Gene structure - - RNA-Seq + resources: + - title: .nan + url: .nan - biocontainers: stringtie + biotools: stringtie bunya: - 2.1.7-gcc-10.3.0 description: Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. + edam-operations: + - term: Transcriptome assembly + url: http://edamontology.org/operation_3258 + - term: RNA-Seq analysis + url: http://edamontology.org/operation_3680 + edam-topics: + - term: Transcriptomics + url: http://edamontology.org/topic_3308 + - term: RNA-seq + url: http://edamontology.org/topic_3170 galaxy: - - description: 'StringTie merge: transcripts' - title: StringTie merge 2.2.1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstringtie%2Fstringtie_merge%2F2.2.1%2Bgalaxy1 - description: 'StringTie: transcript assembly and quantification' - title: StringTie 2.2.1+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstringtie%2Fstringtie%2F2.2.1%2Bgalaxy1 + title: StringTie 2.2.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstringtie%2Fstringtie%2F2.2.3%2Bgalaxy0 + - description: 'StringTie merge: transcripts' + title: StringTie merge 2.2.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstringtie%2Fstringtie_merge%2F2.2.3%2Bgalaxy0 homepage: https://ccb.jhu.edu/software/stringtie/ id: stringtie license: Artistic-2.0 @@ -18007,13 +21802,11 @@ - title: StringTie enables improved reconstruction of a transcriptome from RNA-seq reads url: https://doi.org/10.1038/nbt.3122 - registry-link: stringtie - resource-description: .nan - resource-documentation: .nan - topics: - - Transcriptomics - - RNA-seq + resources: + - title: .nan + url: .nan - biocontainers: subread + biotools: subread bunya: '' description: Subread is a general-purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. It uses a new mapping paradigm called @@ -18021,6 +21814,18 @@ determines if a read should be globally or locally aligned, therefore particularly powerful in mapping RNA-seq reads. It supports indel detection and can map reads with both fixed and variable lengths. + edam-operations: + - term: Read mapping + url: http://edamontology.org/operation_3198 + edam-topics: + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Mapping + url: http://edamontology.org/topic_0102 + - term: Whole genome sequencing + url: http://edamontology.org/topic_3673 + - term: RNA-Seq + url: http://edamontology.org/topic_3170 galaxy: '' homepage: http://subread.sourceforge.net/ id: subread @@ -18036,17 +21841,15 @@ url: https://doi.org/10.1093/nar/gkt214 - title: Simulation-based comprehensive benchmarking of RNA-seq aligners url: https://doi.org/10.1038/nmeth.4106 - registry-link: subread - resource-description: .nan - resource-documentation: .nan - topics: - - Sequencing - - Mapping - - Whole genome sequencing - - RNA-Seq + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Summary Statistics: for any numerical column' title: Summary Statistics 1.1.2 @@ -18059,14 +21862,24 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: super-focus + biotools: super-focus bunya: '' description: An agile homology-based approach using a reduced SEED database to report the subsystems present in metagenomic samples and profile their abundances. + edam-operations: + - term: Sequence feature detection + url: http://edamontology.org/operation_0253 + edam-topics: + - term: DNA + url: http://edamontology.org/topic_0654 + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: '' homepage: http://edwards.sdsu.edu/superfocus/ id: superfocus @@ -18080,19 +21893,24 @@ - title: 'SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data' url: http://www.ncbi.nlm.nih.gov/pubmed/26454280 - registry-link: super-focus - resource-description: .nan - resource-documentation: .nan - topics: - - DNA - - Metagenomics - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: suppa + biotools: suppa bunya: - 2.3--py_2 description: This tool generates Alternative Splicing (AS) events from an annotation and calculates the PSI ("Percentage Spliced In") value for each event exploiting fast quantification of transcript abundances from multiple samples. + edam-operations: + - term: Splicing model analysis + url: http://edamontology.org/operation_2499 + edam-topics: + - term: Transcriptomics + url: http://edamontology.org/topic_3308 + - term: RNA splicing + url: http://edamontology.org/topic_3320 galaxy: '' homepage: https://bitbucket.org/regulatorygenomicsupf/suppa/ id: suppa @@ -18105,13 +21923,11 @@ - title: Leveraging transcript quantification for fast computation of alternative splicing profiles url: https://doi.org/10.1261/rna.051557.115 - registry-link: suppa - resource-description: .nan - resource-documentation: .nan - topics: - - Transcriptomics - - RNA splicing + resources: + - title: .nan + url: .nan - biocontainers: svim-asm + biotools: svim-asm bunya: '' description: 'Structural variant detection from haploid and diploid genome assemblies. @@ -18124,6 +21940,22 @@ from minimap2) and detects five different variant classes between the query assembly and the reference: deletions, insertions, tandem and interspersed duplications and inversions.' + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: Variant calling + url: http://edamontology.org/operation_3227 + - term: Genotyping + url: http://edamontology.org/operation_3196 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Genotype and phenotype + url: http://edamontology.org/topic_0625 + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: DNA polymorphism + url: http://edamontology.org/topic_2885 galaxy: '' homepage: http://github.com/eldariont/svim-asm id: svim-asm @@ -18136,15 +21968,11 @@ publications: - title: 10.1101/2020.10.27.356907 url: https://doi.org/10.1101/2020.10.27.356907 - registry-link: svim-asm - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - Genotype and phenotype - - Sequencing - - DNA polymorphism + resources: + - title: .nan + url: .nan - biocontainers: SyRI + biotools: SyRI bunya: '' description: 'SyRI is tool for finding genomic rearrangements and local sequence differences from whole-genome assemblies. @@ -18160,6 +21988,28 @@ in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions.' + edam-operations: + - term: Haplotype mapping + url: http://edamontology.org/operation_0487 + - term: Variant calling + url: http://edamontology.org/operation_3227 + - term: Genotyping + url: http://edamontology.org/operation_3196 + - term: Sequence assembly + url: http://edamontology.org/operation_0310 + - term: Read mapping + url: http://edamontology.org/operation_3198 + edam-topics: + - term: DNA polymorphism + url: http://edamontology.org/topic_2885 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: DNA structural variation + url: http://edamontology.org/topic_3175 + - term: Mapping + url: http://edamontology.org/topic_0102 + - term: Sequencing + url: http://edamontology.org/topic_3168 galaxy: '' homepage: https://schneebergerlab.github.io/syri/ id: syri @@ -18173,18 +22023,15 @@ - title: 'SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies' url: https://doi.org/10.1186/S13059-019-1911-0 - registry-link: SyRI - resource-description: .nan - resource-documentation: .nan - topics: - - DNA polymorphism - - Sequence assembly - - DNA structural variation - - Mapping - - Sequencing + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'T Test for Two Samples: ' title: T Test for Two Samples 1.0.1 @@ -18197,13 +22044,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Table Compute: computes operations on table data' title: Table Compute 1.2.4+galaxy0 @@ -18216,13 +22065,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Tabular-to-FASTA: converts tabular file to FASTA format' title: Tabular-to-FASTA 1.1.1 @@ -18235,14 +22086,32 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: targetfinder.org + biotools: targetfinder.org bunya: '' description: Targetfinder.org provides a web based resource that allows users to find genes that have a similar expression to a query gene signature. + edam-operations: + - term: Gene prediction + url: http://edamontology.org/operation_2454 + - term: Gene expression profiling + url: http://edamontology.org/operation_0314 + - term: Gene expression analysis + url: http://edamontology.org/operation_2495 + edam-topics: + - term: Gene expression + url: http://edamontology.org/topic_0203 + - term: Transcription factors and regulatory sites + url: http://edamontology.org/topic_0749 + - term: Gene transcripts + url: http://edamontology.org/topic_3512 + - term: Small molecules + url: http://edamontology.org/topic_0154 + - term: Gene regulation + url: http://edamontology.org/topic_0204 galaxy: - description: 'TargetFinder: plant small RNA target prediction tool' title: TargetFinder 1.7.0+galaxy1 @@ -18258,18 +22127,15 @@ - title: 'Targetfinder.org: A resource for systematic discovery of transcription factor target genes' url: http://www.ncbi.nlm.nih.gov/pubmed/20460454 - registry-link: targetfinder.org - resource-description: .nan - resource-documentation: .nan - topics: - - Gene expression - - Transcription factors and regulatory sites - - Gene transcripts - - Small molecules - - Gene regulation + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'TB Variant Filter: M. tuberculosis H37Rv VCF filter' title: TB Variant Filter 0.4.0+galaxy0 @@ -18282,15 +22148,17 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 20220427-linux64 - 20230119-linux64 (D) description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: tbl2asn @@ -18300,13 +22168,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'TB-Profiler Profile: Infer strain types and drug resistance markers from sequences' @@ -18320,18 +22190,20 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'TB Variant Report: - generate HTML report from SnpEff annotated M.tb VCF(s)' - title: TB Variant Report 0.1.10+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftbvcfreport%2Ftbvcfreport%2F0.1.10%2Bgalaxy0 + title: TB Variant Report 1.0.0+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftbvcfreport%2Ftbvcfreport%2F1.0.0%2Bgalaxy0 homepage: '' id: tbvcfreport license: '' @@ -18340,11 +22212,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: tensorflow + biotools: tensorflow bunya: '' description: 'Prediction of cognitive impairment via deep learning trained with multi-center neuropsychological test data. @@ -18360,6 +22232,16 @@ a comprehensive, flexible ecosystem of tools, libraries and community resources that lets researchers push the state-of-the-art in ML and developers easily build and deploy ML powered applications' + edam-operations: + - term: Standardisation and normalisation + url: http://edamontology.org/operation_3435 + edam-topics: + - term: Machine learning + url: http://edamontology.org/topic_3474 + - term: Pathology + url: http://edamontology.org/topic_0634 + - term: Biomarkers + url: http://edamontology.org/topic_3360 galaxy: '' homepage: https://www.tensorflow.org id: tensorflow @@ -18378,14 +22260,11 @@ - title: Prediction of cognitive impairment via deep learning trained with multi-center neuropsychological test data url: https://doi.org/10.1186/S12911-019-0974-X - registry-link: tensorflow - resource-description: .nan - resource-documentation: .nan - topics: - - Machine learning - - Pathology - - Biomarkers + resources: + - title: .nan + url: .nan - biocontainers: TEsorter + biotools: TEsorter bunya: '' description: 'lineage-level classification of transposable elements using conserved protein domains. @@ -18394,6 +22273,20 @@ Note: do not move or hard link TEsorter.py alone to anywhere else, as it rely on database/ and bin/. You can add the directory to PATH or soft link TEsorter.py to PATH' + edam-operations: + - term: Phylogenetic tree reconstruction + url: http://edamontology.org/operation_3478 + edam-topics: + - term: Protein folds and structural domains + url: http://edamontology.org/topic_0736 + - term: Phylogenetics + url: http://edamontology.org/topic_3293 + - term: Transcription factors and regulatory sites + url: http://edamontology.org/topic_0749 + - term: Plant biology + url: http://edamontology.org/topic_0780 + - term: Model organisms + url: http://edamontology.org/topic_0621 galaxy: '' homepage: https://github.com/zhangrengang/TEsorter id: tesorter @@ -18406,18 +22299,15 @@ publications: - title: 10.1101/800177 url: https://doi.org/10.1101/800177 - registry-link: TEsorter - resource-description: .nan - resource-documentation: .nan - topics: - - Protein folds and structural domains - - Phylogenetics - - Transcription factors and regulatory sites - - Plant biology - - Model organisms + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'TEtranscripts: annotates reads to genes and transposable elements' title: TEtranscripts 2.2.3+galaxy0 @@ -18430,13 +22320,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Join: two files' title: Join 9.3+galaxy1 @@ -18503,14 +22395,28 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: ThermoRawFileParser + biotools: ThermoRawFileParser bunya: '' description: Open-source, crossplatform tool that converts Thermo RAW files into open file formats such as MGF and to the HUPO-PSI standard file format mzML + edam-operations: + - term: Conversion + url: http://edamontology.org/operation_3434 + - term: Filtering + url: http://edamontology.org/operation_3695 + - term: Peak detection + url: http://edamontology.org/operation_3215 + edam-topics: + - term: Proteomics + url: http://edamontology.org/topic_0121 + - term: Proteomics experiment + url: http://edamontology.org/topic_3520 + - term: Metabolomics + url: http://edamontology.org/topic_3172 galaxy: - description: 'Thermo: RAW file converter' title: Thermo 1.3.4+galaxy0 @@ -18525,18 +22431,27 @@ publications: - title: 10.1101/622852 url: https://doi.org/10.1101/622852 - registry-link: ThermoRawFileParser - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics - - Proteomics experiment - - Metabolomics + resources: + - title: .nan + url: .nan - biocontainers: tophat + biotools: tophat bunya: '' description: Program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie. A stable SAMtools version is now packaged with the program. + edam-operations: + - term: Splice site prediction + url: http://edamontology.org/operation_0433 + - term: Read mapping + url: http://edamontology.org/operation_3198 + edam-topics: + - term: RNA-Seq + url: http://edamontology.org/topic_3170 + - term: Mapping + url: http://edamontology.org/topic_0102 + - term: Rare diseases + url: http://edamontology.org/topic_3325 galaxy: - description: 'TopHat: Gapped-read mapper for RNA-seq data' title: TopHat 2.1.1 @@ -18557,16 +22472,17 @@ url: https://doi.org/10.1093/bioinformatics/btp120 - title: 10.7490/f1000research.1114334.1 url: https://doi.org/10.7490/f1000research.1114334.1 - registry-link: tophat - resource-description: .nan - resource-documentation: .nan - topics: - - RNA-Seq - - Mapping - - Rare diseases + resources: + - title: .nan + url: .nan - biocontainers: totalview + biotools: totalview bunya: '' description: TotalView is a debugger for High Performance Computing applications. + edam-operations: '' + edam-topics: + - term: Computer science + url: http://edamontology.org/topic_3316 galaxy: '' homepage: https://totalview.io/ id: totalview @@ -18578,18 +22494,37 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: totalview - resource-description: .nan - resource-documentation: .nan - topics: - - Computer science + resources: + - title: .nan + url: .nan - biocontainers: TransDecoder + biotools: TransDecoder bunya: - 5.5.0--pl5321hdfd78af_5 description: TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. + edam-operations: + - term: Coding region prediction + url: http://edamontology.org/operation_0436 + - term: de Novo sequencing + url: http://edamontology.org/operation_3644 + - term: De-novo assembly + url: http://edamontology.org/operation_0524 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Gene transcripts + url: http://edamontology.org/topic_3512 + - term: RNA-Seq + url: http://edamontology.org/topic_3170 + - term: Gene expression + url: http://edamontology.org/topic_0203 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: Whole genome sequencing + url: http://edamontology.org/topic_3673 galaxy: - description: 'TransDecoder: finds coding regions within transcripts' title: TransDecoder 5.5.0+galaxy2 @@ -18602,21 +22537,25 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: TransDecoder - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Gene transcripts - - RNA-Seq - - Gene expression - - Sequence assembly - - Whole genome sequencing + resources: + - title: .nan + url: .nan - biocontainers: transit + biotools: transit bunya: '' description: A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. + edam-operations: + - term: Transposon prediction + url: http://edamontology.org/operation_0427 + edam-topics: + - term: DNA + url: http://edamontology.org/topic_0654 + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Mobile genetic elements + url: http://edamontology.org/topic_0798 galaxy: - description: 'TRANSIT Tn5Gaps: - determine essential genes' title: TRANSIT Tn5Gaps 3.0.2+galaxy1 @@ -18643,16 +22582,19 @@ publications: - title: TRANSIT - A Software Tool for Himar1 TnSeq Analysis url: http://www.ncbi.nlm.nih.gov/pubmed/26447887 - registry-link: transit - resource-description: .nan - resource-documentation: .nan - topics: - - DNA - - Sequencing - - Mobile genetic elements + resources: + - title: .nan + url: .nan - biocontainers: TPP_SPC + biotools: TPP_SPC bunya: '' description: Institute for Systems Biology "Trans-Proteomic Pipeline" + edam-operations: '' + edam-topics: + - term: Proteomics + url: http://edamontology.org/topic_0121 + - term: Proteomics experiment + url: http://edamontology.org/topic_3520 galaxy: - description: 'Protein Prophet: Calculate Protein Prophet statistics on search results' @@ -18691,15 +22633,15 @@ url: http://www.ncbi.nlm.nih.gov/pubmed/21082435 - title: A guided tour of the Trans-Proteomic Pipeline url: http://www.ncbi.nlm.nih.gov/pubmed/20101611 - registry-link: TPP_SPC - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics - - Proteomics experiment + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: transvar @@ -18710,13 +22652,15 @@ - 2.4.0 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: '' id: treeshrink @@ -18727,11 +22671,11 @@ - 1.3.9 pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: trf + biotools: trf bunya: '' description: Tandem Repeats Finder. Find tandem repeats in DNA sequences without the need to specify either the pattern or pattern size. It uses the method of @@ -18740,6 +22684,14 @@ There are no restrictions on the size of the repeats that can be detected. It determines a consensus pattern for the smallest repetitive unit in the tandem repeat. + edam-operations: + - term: Repeat sequence detection + url: http://edamontology.org/operation_0379 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Sequence composition, complexity and repeats + url: http://edamontology.org/topic_0157 galaxy: '' homepage: http://tandem.bu.edu/trf/trf.html id: trf @@ -18752,16 +22704,24 @@ publications: - title: 'Tandem repeats finder: A program to analyze DNA sequences' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC148217 - registry-link: trf - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis - - Sequence composition, complexity and repeats + resources: + - title: .nan + url: .nan - biocontainers: trimal + biotools: trimal bunya: '' description: Tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment. + edam-operations: + - term: Multiple sequence alignment + url: http://edamontology.org/operation_0492 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Sequence sites, features and motifs + url: http://edamontology.org/topic_0160 galaxy: '' homepage: http://trimal.cgenomics.org id: trimal @@ -18775,18 +22735,25 @@ - title: 'trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses' url: http://www.ncbi.nlm.nih.gov/pubmed/19505945 - registry-link: trimal - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis - - Sequencing - - Sequence sites, features and motifs + resources: + - title: .nan + url: .nan - biocontainers: trim_galore + biotools: trim_galore bunya: '' description: A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. + edam-operations: + - term: Sequence trimming + url: http://edamontology.org/operation_3192 + - term: Primer removal + url: http://edamontology.org/operation_3237 + - term: Read pre-processing + url: http://edamontology.org/operation_3219 + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'Trim Galore!: Quality and adapter trimmer of reads' title: Trim Galore! 0.6.7+galaxy0 @@ -18799,15 +22766,24 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: trim_galore - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: trimmomatic + biotools: trimmomatic bunya: - 0.39-java-11 description: A flexible read trimming tool for Illumina NGS data + edam-operations: + - term: Sequence trimming + url: http://edamontology.org/operation_3192 + edam-topics: + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + - term: Data quality management + url: http://edamontology.org/topic_3572 galaxy: - description: 'Trimmomatic: flexible read trimming tool for Illumina NGS data' title: Trimmomatic 0.36.6 @@ -18825,20 +22801,27 @@ - title: 'RobiNA: A user-friendly, integrated software solution for RNA-Seq-based transcriptomics' url: https://doi.org/10.1093/nar/gks540 - registry-link: trimmomatic - resource-description: .nan - resource-documentation: .nan - topics: - - Sequencing - - Sequence analysis - - Data quality management + resources: + - title: .nan + url: .nan - biocontainers: trinity + biotools: trinity bunya: - 2.9.1-foss-2021a - 2.15.1--h6ab5fc9_2 description: Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. + edam-operations: + - term: Transcriptome assembly + url: http://edamontology.org/operation_3258 + edam-topics: + - term: Transcriptomics + url: http://edamontology.org/topic_3308 + - term: Gene expression + url: http://edamontology.org/topic_0203 + - term: Gene transcripts + url: http://edamontology.org/topic_3512 galaxy: - description: 'Generate SuperTranscripts: from a Trinity assembly' title: Generate SuperTranscripts 2.15.1+galaxy0 @@ -18898,19 +22881,24 @@ - title: De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis url: https://doi.org/10.1038/nprot.2013.084 - registry-link: trinity - resource-description: .nan - resource-documentation: .nan - topics: - - Transcriptomics - - Gene expression - - Gene transcripts + resources: + - title: .nan + url: .nan - biocontainers: trinotate + biotools: trinotate bunya: - 3.2.2--pl5321hdfd78af_1 description: Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. + edam-operations: + - term: Gene functional annotation + url: http://edamontology.org/operation_3672 + edam-topics: + - term: Gene expression + url: http://edamontology.org/topic_0203 + - term: Transcriptomics + url: http://edamontology.org/topic_3308 galaxy: - description: 'Trinotate: functional transcript annotation' title: Trinotate 3.2.2+galaxy0 @@ -18926,15 +22914,25 @@ - title: A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors url: https://doi.org/10.1016/j.celrep.2016.12.063 - registry-link: trinotate - resource-description: .nan - resource-documentation: .nan - topics: - - Gene expression - - Transcriptomics + resources: + - title: .nan + url: .nan - biocontainers: trnascan-se + biotools: trnascan-se bunya: '' description: A program for improved detection of transfer RNA genes in genomic sequence. + edam-operations: + - term: tRNA gene prediction + url: http://edamontology.org/operation_0464 + - term: Sequence feature detection + url: http://edamontology.org/operation_0253 + edam-topics: + - term: RNA + url: http://edamontology.org/topic_0099 + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'tRNA prediction: (tRNAscan)' title: tRNA prediction 0.4 @@ -18952,16 +22950,33 @@ url: http://www.ncbi.nlm.nih.gov/pubmed/27174935 - title: 10.1093/nar/25.5.955 url: https://doi.org/10.1093/nar/25.5.955 - registry-link: trnascan-se - resource-description: .nan - resource-documentation: .nan - topics: - - RNA - - Genomics - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: trycycler + biotools: trycycler bunya: '' description: 'Trycycler: consensus long-read assemblies for bacterial genomes' + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: Sequence trimming + url: http://edamontology.org/operation_3192 + - term: Scaffold gap completion + url: http://edamontology.org/operation_3217 + - term: Sequence assembly validation + url: http://edamontology.org/operation_3180 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: DNA + url: http://edamontology.org/topic_0654 + - term: Human biology + url: http://edamontology.org/topic_2815 + - term: Whole genome sequencing + url: http://edamontology.org/topic_3673 + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: - description: 'Trycycler subsample: make a maximally-independent read subsets of an appropiate depth for your genome' @@ -18992,20 +23007,22 @@ publications: - title: 'Trycycler: consensus long-read assemblies for bacterial genomes' url: https://doi.org/10.1186/s13059-021-02483-z - registry-link: trycycler - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - DNA - - Human biology - - Whole genome sequencing - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: UCSC_Genome_Browser_Utilities + biotools: UCSC_Genome_Browser_Utilities bunya: '' description: Utilities for handling sequences and assemblies from the UCSC Genome Browser project. - galaxy: + edam-operations: '' + edam-topics: + - term: Sequence analysis + url: http://edamontology.org/topic_0080 + galaxy: + - description: 'faSplit: Split a FASTA file' + title: faSplit 377 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fucsc_fasplit%2Ffasplit%2F377 - description: 'wigtobigwig: bedGraph or Wig to bigWig converter' title: wigtobigwig 447+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fucsc_wigtobigwig%2Fucsc_wigtobigwig%2F447%2Bgalaxy0 @@ -19030,14 +23047,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: UCSC_Genome_Browser_Utilities - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'UCSC Archaea: table browser' title: UCSC Archaea 1.0.0 @@ -19050,13 +23068,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'UCSC Main: table browser' title: UCSC Main 1.0.0 @@ -19069,13 +23089,23 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: umi-tools + biotools: umi-tools bunya: '' description: Tools for handling Unique Molecular Identifiers in NGS data sets. + edam-operations: + - term: Sequencing quality control + url: http://edamontology.org/operation_3218 + edam-topics: + - term: NGS + url: http://edamontology.org/topic_3168 + - term: Sequence sites, features and motifs + url: http://edamontology.org/topic_0160 + - term: Quality affairs + url: http://edamontology.org/topic_3393 galaxy: - description: 'UMI-tools whitelist: Extract cell barcodes from FASTQ files' title: UMI-tools whitelist 1.1.2+galaxy2 @@ -19103,17 +23133,28 @@ - title: 'UMI-tools: Modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy' url: https://doi.org/10.1101/gr.209601.116 - registry-link: umi-tools - resource-description: .nan - resource-documentation: .nan - topics: - - NGS - - Sequence sites, features and motifs - - Quality affairs + resources: + - title: .nan + url: .nan - biocontainers: unicycler + biotools: unicycler bunya: '' description: A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. + edam-operations: + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: Aggregation + url: http://edamontology.org/operation_3436 + edam-topics: + - term: Microbiology + url: http://edamontology.org/topic_3301 + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: - description: 'Create assemblies with Unicycler: pipeline for bacterial genomes' title: Create assemblies with Unicycler 0.5.0+galaxy1 @@ -19129,17 +23170,27 @@ - title: 'Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads' url: https://doi.org/10.1371/JOURNAL.PCBI.1005595 - registry-link: unicycler - resource-description: .nan - resource-documentation: .nan - topics: - - Microbiology - - Genomics - - Sequencing - - Sequence assembly + resources: + - title: .nan + url: .nan - biocontainers: unipept + biotools: unipept bunya: '' description: Metaproteomics data analysis with a focus on interactive data visualizations. + edam-operations: + - term: Prediction and recognition + url: http://edamontology.org/operation_2423 + - term: Visualisation + url: http://edamontology.org/operation_0337 + edam-topics: + - term: Proteomics + url: http://edamontology.org/topic_0121 + - term: Proteogenomics + url: http://edamontology.org/topic_3922 + - term: Biodiversity + url: http://edamontology.org/topic_3050 + - term: Workflows + url: http://edamontology.org/topic_0769 galaxy: - description: 'Unipept: retrieve taxonomy for peptides' title: Unipept 4.5.1 @@ -19157,17 +23208,15 @@ - title: 'Unipept Desktop: A Faster, More Powerful Metaproteomics Results Analysis Tool' url: https://doi.org/10.1021/ACS.JPROTEOME.0C00855 - registry-link: unipept - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics - - Proteogenomics - - Biodiversity - - Workflows + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'UniProt: download proteome as XML or fasta' title: UniProt 2.4.0 @@ -19180,13 +23229,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'UniProt: ID mapping and retrieval' title: UniProt 0.4 @@ -19199,16 +23250,18 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: - 6.0-gcccore-10.3.0 - 6.0-gcccore-11.3.0 - 6.0-gcccore-12.3.0 (D) description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Unzip: Unzip a file' title: Unzip 6.0+galaxy0 @@ -19221,17 +23274,27 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: vep + biotools: vep bunya: - 107-gcc-11.3.0 description: Tool for predicting effects of variants for any genome in Ensembl or with genome annotation (via GFF). This includes vertebrates and also plants, fungi, protists, metazoa and bacteria. There is a web and a REST API version but the most powerful is the Perl script version. See McLaren et al., 2016, Genome Biology + edam-operations: + - term: SNP annotation + url: http://edamontology.org/operation_3661 + - term: Genetic variation analysis + url: http://edamontology.org/operation_3197 + edam-topics: + - term: Genetic variation + url: http://edamontology.org/topic_0199 + - term: Genomics + url: http://edamontology.org/topic_0622 galaxy: '' homepage: http://www.ensembl.org/vep id: vep @@ -19243,16 +23306,22 @@ publications: - title: The Ensembl Variant Effect Predictor url: https://doi.org/10.1186/s13059-016-0974-4 - registry-link: vep - resource-description: .nan - resource-documentation: .nan - topics: - - Genetic variation - - Genomics + resources: + - title: .nan + url: .nan - biocontainers: varscan + biotools: varscan bunya: '' description: VarScan, an open source tool for variant detection that is compatible with several short read align-ers. + edam-operations: + - term: Variant calling + url: http://edamontology.org/operation_3227 + edam-topics: + - term: Sequencing + url: http://edamontology.org/topic_3168 + - term: DNA polymorphism + url: http://edamontology.org/topic_2885 galaxy: - description: 'VarScan copynumber: Determine relative tumor copy number from tumor-normal pileups' @@ -19282,15 +23351,15 @@ - title: 'VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing' url: https://doi.org/10.1101/gr.129684.111 - registry-link: varscan - resource-description: .nan - resource-documentation: .nan - topics: - - Sequencing - - DNA polymorphism + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'VCF to MAF Custom Track: for display at UCSC' title: VCF to MAF Custom Track 1.0.1 @@ -19303,13 +23372,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Convert VCF to MAF: with vcf2maf' title: Convert VCF to MAF 1.6.21+galaxy1 @@ -19322,14 +23393,22 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: vcflib + biotools: vcflib bunya: - 1.0.3-foss-2021a-r-4.1.0 description: API and command line utilities for the manipulation of VCF files. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + edam-topics: + - term: Genomics + url: http://edamontology.org/topic_0622 + - term: Data management + url: http://edamontology.org/topic_3071 galaxy: - description: 'VCFtoTab-delimited:: Convert VCF data into TAB-delimited format' title: 'VCFtoTab-delimited: 1.0.0_rc3+galaxy0' @@ -19421,18 +23500,26 @@ publications: - title: 10.1101/023754 url: https://doi.org/10.1101/023754 - registry-link: vcflib - resource-description: .nan - resource-documentation: .nan - topics: - - Genomics - - Data management + resources: + - title: .nan + url: .nan - biocontainers: vcftools + biotools: vcftools bunya: - 0.1.16-gcc-10.3.0 - 0.1.16-gcc-11.3.0 (D) description: Provide easily accessible methods for working with complex genetic variation data in the form of VCF files. + edam-operations: + - term: Data handling + url: http://edamontology.org/operation_2409 + - term: Variant filtering + url: http://edamontology.org/operation_3675 + - term: Genetic variation analysis + url: http://edamontology.org/operation_3197 + edam-topics: + - term: Genetic variation + url: http://edamontology.org/topic_0199 galaxy: - description: 'Intersect: multiple VCF datasets' title: Intersect 0.1.1 @@ -19452,15 +23539,20 @@ publications: - title: The variant call format and VCFtools url: https://doi.org/10.1093/bioinformatics/btr330 - registry-link: vcftools - resource-description: .nan - resource-documentation: .nan - topics: - - Genetic variation + resources: + - title: .nan + url: .nan - biocontainers: velvet + biotools: velvet bunya: '' description: A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. + edam-operations: + - term: Formatting + url: http://edamontology.org/operation_0335 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: - description: 'velvetg: Velvet sequence assembler for very short reads' title: velvetg 1.2.10.2 @@ -19483,14 +23575,15 @@ publications: - title: 10.1101/gr.074492.107 url: https://doi.org/10.1101/gr.074492.107 - registry-link: velvet - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://github.com/marbl/verkko id: verkko @@ -19501,13 +23594,15 @@ - '1.1' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://wci.llnl.gov/simulation/computer-codes/visit/ id: visit @@ -19518,17 +23613,19 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Volcano Plot: create a volcano plot' - title: Volcano Plot 0.0.5 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvolcanoplot%2Fvolcanoplot%2F0.0.5 + title: Volcano Plot 0.0.6 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fvolcanoplot%2Fvolcanoplot%2F0.0.6 homepage: '' id: volcanoplot license: '' @@ -19537,17 +23634,27 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: vsearch + biotools: vsearch bunya: '' description: High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. + edam-operations: + - term: DNA mapping + url: http://edamontology.org/operation_2520 + - term: Chimera detection + url: http://edamontology.org/operation_0450 + edam-topics: + - term: Metagenomics + url: http://edamontology.org/topic_3174 + - term: Sequence analysis + url: http://edamontology.org/topic_0080 galaxy: - description: 'VSearch clustering: ' title: VSearch clustering 2.8.3.0 @@ -19583,15 +23690,15 @@ publications: - title: 10.7717/peerj.2584 url: https://doi.org/10.7717/peerj.2584 - registry-link: vsearch - resource-description: .nan - resource-documentation: .nan - topics: - - Metagenomics - - Sequence analysis + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Sequence Logo: generator for fasta (eg Clustal alignments)' title: Sequence Logo 3.5.0 @@ -19604,15 +23711,23 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: whatshap + biotools: whatshap bunya: '' description: Software for phasing genomic variants using DNA sequencing reads, also called haplotype assembly. It is especially suitable for long reads, but works also well with short reads. + edam-operations: + - term: Genotyping + url: http://edamontology.org/operation_3196 + edam-topics: + - term: DNA polymorphism + url: http://edamontology.org/topic_2885 + - term: Sequence assembly + url: http://edamontology.org/topic_0196 galaxy: '' homepage: http://whatshap.readthedocs.io id: whatshap @@ -19628,35 +23743,22 @@ url: https://doi.org/10.1089/cmb.2014.0157 - title: 10.1101/037101 url: https://doi.org/10.1101/037101 - registry-link: whatshap - resource-description: .nan - resource-documentation: .nan - topics: - - DNA polymorphism - - Sequence assembly -- biocontainers: '' - bunya: '' - description: '' - galaxy: - - description: 'Wig/BedGraph-to-bigWig: converter' - title: Wig/BedGraph-to-bigWig 1.1.1 - url: https://usegalaxy.org.au/root?tool_id=wig_to_bigWig - homepage: '' - id: wig_to_bigWig - license: '' - name: wig_to_bigWig - nci-gadi: '' - nci-if89: '' - pawsey: '' - publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: windowmasker + biotools: windowmasker bunya: '' description: windowmasker identifies and masks highly repetitive DNA sequences in a genome, using only the sequence of the genome itself. + edam-operations: + - term: Repeat sequence detection + url: http://edamontology.org/operation_0379 + - term: Repeat sequence analysis + url: http://edamontology.org/operation_0237 + edam-topics: + - term: Sequencing + url: http://edamontology.org/topic_3168 galaxy: - description: 'WindowMasker ustat: Mask sequences using a WindowMasker unit counts table' @@ -19673,17 +23775,22 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: windowmasker - resource-description: .nan - resource-documentation: .nan - topics: - - Sequencing + resources: + - title: .nan + url: .nan - biocontainers: winnowmap + biotools: winnowmap bunya: '' description: Winnowmap is a long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences. Winnowmap development began on top of minimap2 codebase, and since then we have incorporated the following two ideas to improve mapping accuracy within repeats + edam-operations: + - term: Sequence alignment + url: http://edamontology.org/operation_0292 + edam-topics: + - term: Mapping + url: http://edamontology.org/topic_0102 galaxy: '' homepage: https://github.com/marbl/Winnowmap id: winnowmap @@ -19698,16 +23805,37 @@ url: https://doi.org/10.1038/s41592-022-01457-8 - title: Weighted minimizer sampling improves long read mapping url: https://doi.org/10.1093/bioinformatics/btaa435 - registry-link: winnowmap - resource-description: .nan - resource-documentation: .nan - topics: - - Mapping + resources: + - title: .nan + url: .nan - biocontainers: workflow4metabolomics + biotools: workflow4metabolomics bunya: '' description: First fully open-source and collaborative online platform for computational metabolomics. It includes preprocessing, normalization, quality control, statistical analysis of LC/MS, FIA-MS, GC/MS and NMR data. + edam-operations: + - term: Visualisation + url: http://edamontology.org/operation_0337 + - term: Statistical calculation + url: http://edamontology.org/operation_2238 + - term: Chromatogram visualisation + url: http://edamontology.org/operation_3203 + - term: Spectral analysis + url: http://edamontology.org/operation_3214 + - term: Annotation + url: http://edamontology.org/operation_0226 + - term: Mass spectrum visualisation + url: http://edamontology.org/operation_3694 + - term: Enrichment analysis + url: http://edamontology.org/operation_3501 + edam-topics: + - term: Systems biology + url: http://edamontology.org/topic_2259 + - term: Metabolomics + url: http://edamontology.org/topic_3172 + - term: Computational biology + url: http://edamontology.org/topic_3307 galaxy: - description: 'Determine_batch_correction: to choose between linear, lowess and loess methods' @@ -19789,16 +23917,15 @@ MS, GC\u2013MS, and NMR data analysis workflows with the Workflow4Metabolomics\ \ 3.0 Galaxy online infrastructure for metabolomics" url: https://doi.org/10.1016/j.biocel.2017.07.002 - registry-link: workflow4metabolomics - resource-description: .nan - resource-documentation: .nan - topics: - - Systems biology - - Metabolomics - - Computational biology + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'WormBase: server' title: WormBase 1.0.1 @@ -19811,13 +23938,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'NetCDF xarray Metadata Info: summarize content of a Netcdf file' title: NetCDF xarray Metadata Info 0.15.1 @@ -19834,16 +23963,38 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: xcms + biotools: xcms bunya: '' description: Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling. + edam-operations: + - term: Mass spectrum visualisation + url: http://edamontology.org/operation_3694 + - term: Label-free quantification + url: http://edamontology.org/operation_3634 + - term: Validation + url: http://edamontology.org/operation_2428 + - term: Filtering + url: http://edamontology.org/operation_3695 + - term: Chromatographic alignment + url: http://edamontology.org/operation_3628 + - term: Peak detection + url: http://edamontology.org/operation_3215 + - term: Chromatogram visualisation + url: http://edamontology.org/operation_3203 + edam-topics: + - term: Biological imaging + url: http://edamontology.org/topic_3383 + - term: Data visualisation + url: http://edamontology.org/topic_0092 + - term: Metabolomics + url: http://edamontology.org/topic_3172 galaxy: - description: 'xcms get a sampleMetadata file: which need to be filled with extra information' @@ -19884,16 +24035,15 @@ - title: Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data url: https://doi.org/10.1093/bioinformatics/btq441 - registry-link: xcms - resource-description: .nan - resource-documentation: .nan - topics: - - Biological imaging - - Data visualisation - - Metabolomics + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: '' homepage: https://github.com/AustralianBioCommons/xml4ena id: xml4ena @@ -19903,11 +24053,11 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: Documentation link - resource-documentation: https://github.com/AustralianBioCommons/xml4ena - topics: '' + resources: + - title: Documentation link + url: https://github.com/AustralianBioCommons/xml4ena - biocontainers: xpore + biotools: xpore bunya: - 2.1--pyh5e36f6f_0 description: 'Detection of differential RNA modifications from direct RNA sequencing @@ -19916,6 +24066,24 @@ Python package for detection of differential RNA modifications from direct RNA sequencing.' + edam-operations: + - term: Quantification + url: http://edamontology.org/operation_3799 + - term: Expression analysis + url: http://edamontology.org/operation_2495 + - term: DMR identification + url: http://edamontology.org/operation_3809 + edam-topics: + - term: RNA-Seq + url: http://edamontology.org/topic_3170 + - term: RNA + url: http://edamontology.org/topic_0099 + - term: Gene expression + url: http://edamontology.org/topic_0203 + - term: Genotype and phenotype + url: http://edamontology.org/topic_0625 + - term: Molecular interactions, pathways and networks + url: http://edamontology.org/topic_0602 galaxy: '' homepage: https://github.com/GoekeLab/xpore id: xpore @@ -19927,18 +24095,29 @@ publications: - title: 10.1101/2020.06.18.160010 url: https://doi.org/10.1101/2020.06.18.160010 - registry-link: xpore - resource-description: .nan - resource-documentation: .nan - topics: - - RNA-Seq - - RNA - - Gene expression - - Genotype and phenotype - - Molecular interactions, pathways and networks + resources: + - title: .nan + url: .nan - biocontainers: xtandem + biotools: xtandem bunya: '' description: Matches tandem mass spectra with peptide sequences. + edam-operations: + - term: Blind peptide database search + url: http://edamontology.org/operation_3647 + - term: PTM identification + url: http://edamontology.org/operation_3645 + - term: Peptide identification + url: http://edamontology.org/operation_3631 + - term: Peptide database search + url: http://edamontology.org/operation_3646 + - term: Protein identification + url: http://edamontology.org/operation_3767 + edam-topics: + - term: Proteomics + url: http://edamontology.org/topic_0121 + - term: Proteomics experiment + url: http://edamontology.org/topic_3520 galaxy: - description: 'X!Tandem MSMS Search: Run an X!Tandem Search' title: X!Tandem MSMS Search 1.1.1 @@ -19956,15 +24135,15 @@ publications: - title: 'TANDEM: Matching proteins with tandem mass spectra' url: https://doi.org/10.1093/bioinformatics/bth092 - registry-link: xtandem - resource-description: .nan - resource-documentation: .nan - topics: - - Proteomics - - Proteomics experiment + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'Plotting tool: for multiple series and graph types' title: Plotting tool 1.0.2 @@ -19977,15 +24156,27 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: yahs + biotools: yahs bunya: '' description: YaHS is scaffolding tool using Hi-C data. It relies on a new algorithm for contig joining detection which considers the topological distribution of Hi-C signals aiming to distinguish real interaction signals from mapping noises. + edam-operations: + - term: Scaffolding + url: http://edamontology.org/operation_3216 + - term: Genome assembly + url: http://edamontology.org/operation_0525 + - term: De-novo assembly + url: http://edamontology.org/operation_0524 + edam-topics: + - term: Sequence assembly + url: http://edamontology.org/topic_0196 + - term: DNA binding sites + url: http://edamontology.org/topic_3125 galaxy: - description: 'YAHS: yet another HI-C scaffolding tool' title: YAHS 1.2a.2+galaxy1 @@ -20001,15 +24192,15 @@ publications: - title: 10.1101/2022.06.09.495093 url: https://doi.org/10.1101/2022.06.09.495093 - registry-link: yahs - resource-description: .nan - resource-documentation: .nan - topics: - - Sequence assembly - - DNA binding sites + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'YeastMine: server' title: YeastMine 1.0.0 @@ -20022,13 +24213,15 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan - biocontainers: '' + biotools: '' bunya: '' description: '' + edam-operations: '' + edam-topics: '' galaxy: - description: 'ZebrafishMine: server' title: ZebrafishMine 1.0.0 @@ -20041,7 +24234,6 @@ nci-if89: '' pawsey: '' publications: '' - registry-link: '' - resource-description: .nan - resource-documentation: .nan - topics: '' + resources: + - title: .nan + url: .nan