diff --git a/communities/spoc/metadata/categories b/communities/spoc/metadata/categories index b76ed2c4..a86034b3 100644 --- a/communities/spoc/metadata/categories +++ b/communities/spoc/metadata/categories @@ -1,2 +1,3 @@ Single Cell Spatial Omics +Transcriptomics \ No newline at end of file diff --git a/communities/spoc/metadata/tool_status.tsv b/communities/spoc/metadata/tool_status.tsv new file mode 100644 index 00000000..7faf75ee --- /dev/null +++ b/communities/spoc/metadata/tool_status.tsv @@ -0,0 +1,100 @@ +aegean FALSE FALSE +anndata TRUE FALSE +arriba FALSE FALSE +askor FALSE FALSE +bamparse FALSE FALSE +baredsc TRUE FALSE +bctools FALSE FALSE +brew3r_r FALSE FALSE +cell-types-analysis TRUE FALSE +cemitool TRUE FALSE +cherri FALSE FALSE +chira FALSE FALSE +cite_seq_count TRUE FALSE +cosg TRUE FALSE +cpat FALSE FALSE +cpm_tpm_rpk FALSE FALSE +crosscontamination_barcode_filter TRUE FALSE +cuffcompare FALSE FALSE +cuffdiff FALSE FALSE +cufflinks FALSE FALSE +cuffmerge FALSE FALSE +cuffnorm FALSE FALSE +cuffquant FALSE FALSE +data-hca TRUE FALSE +data-scxa TRUE FALSE +decoupler TRUE FALSE +deg_annotate TRUE FALSE +deseq2 TRUE FALSE +deseq2_normalization TRUE FALSE +dexseq TRUE FALSE +dropletutils TRUE FALSE +edger TRUE FALSE +egsea TRUE FALSE +episcanpy TRUE FALSE +fastq_provider FALSE FALSE +fastq_utils FALSE FALSE +featurecounts FALSE FALSE +fgsea TRUE FALSE +garnett TRUE FALSE +genomic_super_signature FALSE FALSE +gffcompare FALSE FALSE +gsc_filter_cells TRUE FALSE +gsc_filter_genes TRUE FALSE +gsc_gene_expression_correlations TRUE FALSE +gsc_high_dimensions_visualisation TRUE FALSE +gsc_mannwhitney_de TRUE FALSE +gsc_scran_normalize TRUE FALSE +gsc_signature_score TRUE FALSE +heinz TRUE FALSE +infercnv TRUE FALSE +isoformswitchanalyzer FALSE FALSE +kallisto FALSE FALSE +limma_voom FALSE FALSE +masigpro FALSE FALSE +mircounts FALSE FALSE +monocle3 TRUE FALSE +multigsea TRUE FALSE +music_deconvolution TRUE FALSE +nugen_nudup FALSE FALSE +pathifier FALSE FALSE +pizzly FALSE FALSE +psiclass FALSE FALSE +pyscenic TRUE FALSE +qualimap FALSE FALSE +raceid TRUE FALSE +repenrich FALSE FALSE +repenrich2 FALSE FALSE +rgrnastar TRUE FALSE +ribowaltz FALSE FALSE +rsem FALSE FALSE +rseqc FALSE FALSE +ruvseq FALSE FALSE +salmon TRUE FALSE +sashimi_plot FALSE FALSE +sc3 TRUE FALSE +scanpy TRUE FALSE +scater TRUE FALSE +sccaf TRUE FALSE +sceasy TRUE FALSE +schicexplorer TRUE FALSE +scmap TRUE FALSE +scpipe TRUE FALSE +scpred TRUE FALSE +seurat TRUE FALSE +sinto TRUE FALSE +slamdunk FALSE FALSE +sleuth FALSE FALSE +snapatac2 TRUE FALSE +spapros TRUE FALSE +star_fusion FALSE FALSE +stringtie FALSE FALSE +tophat_fusion_post FALSE FALSE +transdecoder FALSE FALSE +trinity FALSE FALSE +trinotate FALSE FALSE +tximport FALSE FALSE +ucsc-cell-browser TRUE FALSE +umi_tools TRUE FALSE +velocyto TRUE FALSE +volcanoplot TRUE FALSE \ No newline at end of file diff --git a/communities/spoc/resources/tools.html b/communities/spoc/resources/tools.html index fee090cf..2e8c7922 100644 --- a/communities/spoc/resources/tools.html +++ b/communities/spoc/resources/tools.html @@ -213,7 +213,7 @@ 69688 3002 3003 - + False @@ -292,7 +292,165 @@ 161 22 22 + False + + + + cell-types-analysis + ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals + Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis + + + + + + + + To update + + Transcriptomics, RNA, Statistics + suite_cell_types_analysis + 2020-04-07 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis + 1.1.1 + cell-types-analysis + 0.1.11 + + + 0 + 0 + 6 + 0 + 0 + 0 + 6 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 8 + 8 + 4 + 4 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 8 + 8 + 4 + 4 + False + + + + cemitool + cemitool + Gene co-expression network analysis tool + cemitool + cemitool + CEMiTool + It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. + Enrichment analysis, Pathway or network analysis + Gene expression, Transcriptomics, Microarray experiment + Up-to-date + https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html + Transcriptomics, RNA, Statistics + cemitool + 2022-10-10 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool + https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool + 1.26.0 + bioconductor-cemitool + 1.26.0 + Enrichment analysis, Pathway or network analysis + Transcriptomics, Microarray experiment + 1 + 0 + 1 + 0 + 1 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 0 + 225 + 225 + 32 + 32 + 271 + 271 + 61 + 61 + 0 + 0 + 0 + 0 + 496 + 496 + 93 + 93 + False @@ -371,7 +529,7 @@ 48 10 10 - + False @@ -450,40 +608,39 @@ 0 0 0 - + False - dropletutils - dropletutils - DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data - dropletutils - dropletutils + crosscontamination_barcode_filter + crosscontamination_barcode_filter + Barcode contamination discovery tool + + + + + + - DropletUtils - 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. - Loading, Community profiling - Gene expression, RNA-seq, Sequencing, Transcriptomics To update - https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html - Single Cell, Sequence Analysis - dropletutils - 2019-09-02 + + Transcriptomics, Visualization + crosscontamination_barcode_filter + 2018-07-27 iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ - https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils - 1.10.0 - bioconductor-dropletutils - 1.22.0 + https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter + https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter + 0.3 + r-ggplot2 + 2.2.1 + - Sequencing, Transcriptomics - 1 - 1 - 1 - 1 1 + 0 1 + 0 1 + 0 1 0 0 @@ -498,7 +655,8 @@ 0 0 0 - 1 + 0 + 0 0 0 0 @@ -513,60 +671,56 @@ 1 1 0 - 4413 - 4442 - 430 - 431 - 4403 - 4403 - 255 - 255 - 1816 - 1816 - 33 - 33 - 10632 - 10661 - 718 - 719 - + 276 + 390 + 61 + 76 + 131 + 131 + 42 + 42 + 0 + 0 + 0 + 0 + 407 + 521 + 103 + 118 + False - episcanpy - episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess - EpiScanpy – Epigenomics single cell analysis in python - episcanpy - episcanpy + data-hca + hca_matrix_downloader + Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects + + + + + + - epiScanpy - Epigenomics Single Cell Analysis in Python. - Enrichment analysis, Imputation - Epigenomics, Cell biology, DNA To update - https://github.com/colomemaria/epiScanpy - Single Cell, Epigenetics - episcanpy - 2023-03-22 - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ - https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy - 0.3.2 - episcanpy - 0.4.0 - Enrichment analysis, Imputation - Epigenomics, Cell biology, DNA - 3 - 3 - 3 + + Transcriptomics, Sequence Analysis + suite_human_cell_atlas_tools + 2019-07-02 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca + v0.0.4+galaxy0 + hca-matrix-downloader + 0.0.4 + + 0 - 3 - 3 - 3 0 + 1 0 0 0 + 1 0 0 0 @@ -589,32 +743,36 @@ 0 0 0 - 3 0 0 - 880 - 880 - 80 - 80 - 221 - 221 - 37 - 37 - 49 - 49 + 0 + 0 + 1 + 1 + 0 + 441 + 451 + 83 + 87 3 3 - 1150 - 1150 - 120 - 120 - + 2 + 2 + 0 + 0 + 0 + 0 + 444 + 454 + 85 + 89 + False - raceid - raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory - RaceID3, StemID2, FateID - scRNA analysis + data-scxa + retrieve_scxa + Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home @@ -623,21 +781,2075 @@ To update - https://github.com/dgrun/RaceID3_StemID2_package/ - Single Cell, Transcriptomics - 2021-04-14 - iuc - https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 - https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid - 0.2.3 - r-raceid - 0.1.3 + Transcriptomics, Sequence Analysis + suite_ebi_expression_atlas + 2019-07-02 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa + v0.0.2+galaxy2 + wget + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 0 + 867 + 877 + 213 + 216 + 339 + 339 + 94 + 94 + 64 + 64 + 5 + 5 + 1270 + 1280 + 312 + 315 + False + + + + decoupler + score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk + decoupler - Ensemble of methods to infer biological activities + + + + + + + + To update + https://decoupler-py.readthedocs.io/en/latest/ + Transcriptomics + suite_decoupler + 2023-09-24 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler + 1.4.0+galaxy3 + decoupler + 1.5.0 + + + 0 + 0 + 1 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 54 + 54 + 6 + 6 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 54 + 54 + 6 + 6 + False + + + + deg_annotate + deg_annotate + Annotate DESeq2/DEXSeq output tables + + + + + + + + To update + https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate + Transcriptomics + deg_annotate + 2018-11-22 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate + https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate + 1.1.0 + bedtools + 2.31.1 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 1 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 1 + 0 + 22774 + 23146 + 4084 + 4155 + 33972 + 33972 + 5372 + 5372 + 4236 + 4236 + 846 + 846 + 60982 + 61354 + 10302 + 10373 + False + + + + deseq2 + deseq2 + Differential gene expression analysis based on the negative binomial distribution + DESeq2 + DESeq2 + + DESeq2 + 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. + Differential gene expression analysis, RNA-Seq analysis + RNA-Seq + To update + https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html + Transcriptomics, RNA, Statistics + deseq2 + 2018-11-15 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 + https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 + 2.11.40.8 + bioconductor-deseq2 + 1.42.0 + Differential gene expression analysis, RNA-Seq analysis + RNA-Seq + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 1 + 0 + 0 + 1 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 1 + 0 + 97434 + 109474 + 11355 + 12514 + 183905 + 246475 + 24951 + 31957 + 18551 + 20166 + 2647 + 2905 + 299890 + 376115 + 38953 + 47376 + False + + + + deseq2_normalization + deseq2_normalization + Normalizes gene hitlists + + + + + + + + To update + http://artbio.fr + RNA, Transcriptomics, Sequence Analysis, Statistics + deseq2_normalization + 2018-01-05 + artbio + https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization + https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization + 1.40.2+galaxy0 + bioconductor-deseq2 + 1.42.0 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + False + + + + dexseq + dexseq, dexseq_count, plotdexseq + Inference of differential exon usage in RNA-Seq + dexseq + dexseq + + DEXSeq + The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model 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. + Enrichment analysis, Exonic splicing enhancer prediction + RNA-Seq + Up-to-date + https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html + Transcriptomics, RNA, Statistics + dexseq + 2018-05-02 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq + https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq + 1.48.0 + bioconductor-dexseq + 1.48.0 + Enrichment analysis, Exonic splicing enhancer prediction + RNA-Seq + 3 + 3 + 3 + 3 + 3 + 3 + 3 + 3 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 3 + 3 + 3 + 0 + 14874 + 16927 + 533 + 837 + 18475 + 28854 + 1403 + 2568 + 3854 + 4271 + 141 + 163 + 37203 + 50052 + 2077 + 3568 + False + + + + dropletutils + dropletutils_empty_drops, dropletutils_read_10x + De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 + + + + + + + + To update + + Transcriptomics, RNA, Statistics, Sequence Analysis + suite_dropletutils + 2019-01-22 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils + 1.0.4 + dropletutils-scripts + 0.0.5 + + + 2 + 2 + 2 + 0 + 2 + 2 + 2 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 2 + 0 + 0 + 1900 + 1901 + 412 + 413 + 609 + 609 + 131 + 131 + 0 + 0 + 0 + 0 + 2509 + 2510 + 543 + 544 + False + + + + dropletutils + dropletutils + DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data + dropletutils + dropletutils + + DropletUtils + 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. + Loading, Community profiling + Gene expression, RNA-seq, Sequencing, Transcriptomics + To update + https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html + Single Cell, Sequence Analysis + dropletutils + 2019-09-02 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils + 1.10.0 + bioconductor-dropletutils + 1.22.0 + + Sequencing, Transcriptomics + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 1 + 0 + 4413 + 4442 + 430 + 431 + 4403 + 4403 + 255 + 255 + 1816 + 1816 + 33 + 33 + 10632 + 10661 + 718 + 719 + False + + + + edger + edger + Perform RNA-Seq differential expression analysis using edgeR pipeline + edger + edger + + edgeR + Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact 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. + Differential gene expression analysis + Genetics, RNA-Seq, ChIP-seq + To update + http://bioconductor.org/packages/release/bioc/html/edgeR.html + Transcriptomics, RNA, Statistics + edger + 2019-02-08 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger + https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger + 3.36.0 + bioconductor-edger + 4.0.16 + Differential gene expression analysis + Genetics, RNA-Seq, ChIP-seq + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 1 + 0 + 0 + 1 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 1 + 0 + 19294 + 20905 + 2423 + 2618 + 48876 + 58723 + 6341 + 7527 + 8010 + 8705 + 846 + 892 + 76180 + 88333 + 9610 + 11037 + False + + + + egsea + egsea + This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing + egsea + egsea + + EGSEA + This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. + Gene set testing + Systems biology + To update + https://bioconductor.org/packages/release/bioc/html/EGSEA.html + Transcriptomics, RNA, Statistics + egsea + 2018-01-01 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea + https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea + 1.20.0 + bioconductor-egsea + 1.28.0 + Gene set testing + Systems biology + 1 + 1 + 1 + 0 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 1 + 0 + 2809 + 3060 + 371 + 402 + 5179 + 5179 + 759 + 759 + 1931 + 1931 + 226 + 226 + 9919 + 10170 + 1356 + 1387 + False + + + + episcanpy + episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess + EpiScanpy – Epigenomics single cell analysis in python + episcanpy + episcanpy + + epiScanpy + Epigenomics Single Cell Analysis in Python. + Enrichment analysis, Imputation + Epigenomics, Cell biology, DNA + To update + https://github.com/colomemaria/epiScanpy + Single Cell, Epigenetics + episcanpy + 2023-03-22 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ + https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy + 0.3.2 + episcanpy + 0.4.0 + Enrichment analysis, Imputation + Epigenomics, Cell biology, DNA + 3 + 3 + 3 + 0 + 3 + 3 + 3 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 3 + 0 + 0 + 880 + 880 + 80 + 80 + 221 + 221 + 37 + 37 + 49 + 49 + 3 + 3 + 1150 + 1150 + 120 + 120 + False + + + + fgsea + fgsea + Perform gene set testing using fgsea + fgsea + fgsea + + fgsea + 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. + Gene-set enrichment analysis + Genetics + To update + https://bioconductor.org/packages/release/bioc/html/fgsea.html + Visualization, Transcriptomics, Statistics + fgsea + 2018-10-19 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea + https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea + 1.8.0+galaxy1 + bioconductor-fgsea + 1.28.0 + Gene-set enrichment analysis + Genetics + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 1 + 0 + 5618 + 5820 + 582 + 607 + 21673 + 21673 + 938 + 938 + 869 + 869 + 110 + 110 + 28160 + 28362 + 1630 + 1655 + False + + + + garnett + garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file + De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 + + + + + + + + To update + + Transcriptomics, RNA, Statistics, Sequence Analysis + suite_garnett + 2020-04-03 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett + 0.2.8 + garnett-cli + 0.0.5 + + + 0 + 0 + 7 + 0 + 0 + 0 + 7 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 27 + 27 + 11 + 11 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 27 + 27 + 11 + 11 + False + + + + gsc_filter_cells + filter_cells + Filter single cell RNAseq data on libray depth and number of detected genes + + + + + + + + To update + http://artbio.fr + Transcriptomics + gsc_filter_cells + 2019-06-23 + artbio + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells + 4.3.1+galaxy0 + r-optparse + 1.3.2 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + False + + + + gsc_filter_genes + filter_genes + Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data + + + + + + + + To update + http://artbio.fr + Transcriptomics + gsc_filter_genes + 2019-06-23 + artbio + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes + 4.3.1+galaxy0 + r-optparse + 1.3.2 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + False + + + + gsc_gene_expression_correlations + single_cell_gene_expression_correlations + Compute single-cell paire-wise gene expressions correlations + + + + + + + + To update + http://artbio.fr + Transcriptomics + gsc_gene_expression_correlations + 2019-06-24 + artbio + https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations + 4.3.1+galaxy0 + r-optparse + 1.3.2 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + False + + + + gsc_high_dimensions_visualisation + high_dimensions_visualisation + Generates PCA, t-SNE and HCPC visualisation + + + + + + + + To update + http://artbio.fr + Transcriptomics, Visualization + gsc_high_dimensions_visualisation + 2019-07-09 + artbio + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation + 4.3+galaxy0 + r-optparse + 1.3.2 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + False + + + + gsc_mannwhitney_de + mannwhitney_de + Perform a mann-whitney differential testing between two sets of gene expression data + + + + + + + + To update + http://artbio.fr + Transcriptomics + gsc_mannwhitney_de + 2019-06-23 + artbio + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de + 4.1.3+galaxy0 + r-optparse + 1.3.2 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + False + + + + gsc_scran_normalize + scran_normalize + Normalize raw counts using scran + + + + + + + + To update + http://artbio.fr + Transcriptomics + gsc_scran_normalize + 2019-09-23 + artbio + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize + 1.28.1+galaxy0 + bioconductor-scran + 1.30.0 + + + 1 + 1 + 1 + 0 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 0 + 89 + 89 + 24 + 24 + 3 + 3 + 2 + 2 + 10 + 10 + 2 + 2 + 102 + 102 + 28 + 28 + False + + + + gsc_signature_score + signature_score + Compute signature scores from single cell RNAseq data + + + + + + + + To update + http://artbio.fr + Transcriptomics + gsc_signature_score + 2019-06-23 + artbio + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score + https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score + 2.3.9+galaxy0 + r-optparse + 1.3.2 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + False + + + + heinz + heinz_bum, heinz, heinz_scoring, heinz_visualization + An algorithm for identification of the optimal scoring subnetwork. + heinz + heinz, bionet + + Heinz + Tool for single-species active module discovery. + Pathway or network analysis + Genetics, Gene expression, Molecular interactions, pathways and networks + To update + https://github.com/ls-cwi/heinz + Transcriptomics, Visualization, Statistics + heinz + 2018-06-11 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz + https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz + 1.0 + bioconductor-bionet + 1.62.0 + Pathway or network analysis + Genetics, Gene expression, Molecular interactions, pathways and networks + 4 + 4 + 4 + 0 + 4 + 4 + 4 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 4 + 4 + 4 + 0 + 1281 + 1434 + 367 + 442 + 1559 + 1559 + 636 + 636 + 678 + 678 + 52 + 52 + 3518 + 3671 + 1055 + 1130 + False + + + + infercnv + infercnv + Infer Copy Number Variation from Single-Cell RNA-Seq Data + + + + + + + + Up-to-date + https://github.com/broadinstitute/infercnv + Transcriptomics, Variant Analysis + infercnv + 2024-07-23 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv + https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv + 1.20.0 + bioconductor-infercnv + 1.20.0 + + + 0 + 0 + 1 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 10 + 10 + 2 + 2 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 10 + 10 + 2 + 2 + False + + + + monocle3 + monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers + De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. + + + + + + + + To update + + Transcriptomics, RNA, Statistics, Sequence Analysis + suite_monocle3 + 2019-09-09 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 + 0.1.4 + monocle3-cli + 0.0.9 + + + 9 + 0 + 9 + 0 + 9 + 0 + 9 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 3610 + 3610 + 559 + 559 + 1728 + 1728 + 434 + 434 + 0 + 0 + 0 + 0 + 5338 + 5338 + 993 + 993 + False + + + + multigsea + multigsea + GSEA-based pathway enrichment analysis for multi-omics data + multiGSEA + multiGSEA + + multiGSEA + A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. + Gene-set enrichment analysis, Aggregation, Pathway analysis + Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules + Up-to-date + https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html + Transcriptomics, Proteomics, Statistics + multigsea + 2023-06-07 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea + https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea + 1.12.0 + bioconductor-multigsea + 1.12.0 + Gene-set enrichment analysis, Aggregation, Pathway analysis + Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules + 0 + 0 + 1 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 0 + 106 + 106 + 25 + 25 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 106 + 106 + 25 + 25 + False + + + + music_deconvolution + music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution + Multi-subject Single Cell deconvolution (MuSiC) + + + + + + + + Up-to-date + https://github.com/xuranw/MuSiC + Transcriptomics + music + 2021-09-12 + bgruening + https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ + https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution + 0.1.1 + music-deconvolution + 0.1.1 + + + 5 + 5 + 4 + 0 + 5 + 5 + 4 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 5 + 0 + 0 + 2801 + 2801 + 289 + 289 + 364 + 364 + 80 + 80 + 1357 + 1357 + 21 + 21 + 4522 + 4522 + 390 + 390 + False + + + + pyscenic + pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn + PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ + + + + + + + + To update + + Transcriptomics, RNA, Sequence Analysis + suite_pyscenic + 2024-08-20 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic + 0.12.1 + + + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + False + + + + raceid + raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory + RaceID3, StemID2, FateID - scRNA analysis + + + + + + + + To update + https://github.com/dgrun/RaceID3_StemID2_package/ + Single Cell, Transcriptomics + + 2021-04-14 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 + https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid + 0.2.3 + r-raceid + 0.1.3 + + + 5 + 5 5 - 5 - 5 1 5 5 @@ -687,7 +2899,244 @@ 9414 1507 1630 + False + + + + rgrnastar + rna_star, rna_starsolo + RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper + star + star + + STAR + Ultrafast universal RNA-seq data aligner + Sequence alignment + RNA-Seq, Transcriptomics + To update + https://github.com/alexdobin/STAR + Next Gen Mappers, Transcriptomics + rgrnastar + 2023-02-27 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar + https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar + 2.7.11a + star + 2.7.11b + Sequence alignment + RNA-Seq, Transcriptomics + 2 + 2 + 2 + 2 + 2 + 2 + 2 + 2 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 1 + 0 + 0 + 2 + 0 + 0 + 0 + 2 + 0 + 0 + 0 + 0 + 0 + 0 + 2 + 2 + 2 + 0 + 438078 + 473957 + 10142 + 10900 + 325474 + 403925 + 15284 + 18791 + 49662 + 53138 + 1359 + 1449 + 813214 + 931020 + 26785 + 31140 + False + + + + salmon + alevin, salmon, salmonquantmerge + Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. + salmon + salmon + + Salmon + A tool for transcript expression quantification from RNA-seq data + Sequence composition calculation, RNA-Seq quantification, Gene expression analysis + RNA-Seq, Gene expression, Transcriptomics + To update + https://github.com/COMBINE-lab/salmon + Sequence Analysis, RNA, Transcriptomics + + 2019-09-18 + bgruening + https://github.com/bgruening/galaxytools/tree/master/tools/salmon + https://github.com/bgruening/galaxytools/tree/master/tools/salmon + 1.10.1 + salmon + 1.10.3 + Sequence composition calculation, RNA-Seq quantification, Gene expression analysis + RNA-Seq, Transcriptomics + 2 + 2 + 3 + 1 + 2 + 2 + 3 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 2 + 1 + 0 + 0 + 1 + 0 + 0 + 0 + 2 + 0 + 0 + 0 + 0 + 0 + 0 + 3 + 3 + 3 + 0 + 73085 + 77081 + 2243 + 2319 + 90634 + 122835 + 3402 + 4726 + 13371 + 15818 + 513 + 586 + 177090 + 215734 + 6158 + 7631 + False + + + + sc3 + sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare + De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. + + + + + + + To update + + Transcriptomics, RNA, Statistics, Sequence Analysis + suite_sc3 + 2018-11-05 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 + 1.8.0 + sc3-scripts + 0.0.6 + + + 0 + 0 + 7 + 0 + 0 + 0 + 7 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 13 + 13 + 10 + 10 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 13 + 13 + 10 + 10 + False @@ -718,8 +3167,166 @@ 6 6 0 - 6 - 6 + 6 + 6 + 6 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 6 + 6 + 6 + 0 + 63789 + 64034 + 2543 + 2547 + 29962 + 29962 + 1185 + 1185 + 18028 + 18028 + 379 + 379 + 111779 + 112024 + 4107 + 4111 + False + + + + scanpy + anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data + scanpy-scripts, command-line wrapper scripts around Scanpy. + + + + + + + + To update + https://scanpy.readthedocs.io + Transcriptomics, Sequence Analysis, RNA + scanpy_scripts + 2020-09-29 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy + 1.9.3 + scanpy-scripts + 1.9.301 + + + 27 + 27 + 27 + 0 + 27 + 27 + 27 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 14 + 13 + 0 + 45501 + 45666 + 4832 + 4868 + 7304 + 7304 + 1846 + 1846 + 3106 + 3106 + 457 + 457 + 55911 + 56076 + 7135 + 7171 + False + + + + scater + scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results + De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. + + + + + + + + To update + + Transcriptomics, RNA, Statistics, Sequence Analysis + suite_scater + 2018-10-11 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater + 1.10.0 + scater-scripts + 0.0.5 + + + 1 + 2 + 6 + 0 + 1 + 2 6 0 0 @@ -746,27 +3353,27 @@ 0 0 0 - 6 - 6 - 6 + 2 + 2 + 2 0 - 63789 - 64034 - 2543 - 2547 - 29962 - 29962 - 1185 - 1185 - 18028 - 18028 - 379 - 379 - 111779 - 112024 - 4107 - 4111 - + 381 + 388 + 99 + 100 + 0 + 0 + 0 + 0 + 297 + 297 + 9 + 9 + 678 + 685 + 108 + 109 + False @@ -845,7 +3452,165 @@ 2274 379 380 + False + + + + sccaf + run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out + SCCAF: Single Cell Clustering Assessment Framework. + + + + + + + + To update + https://github.com/sccaf/sccaf + Transcriptomics + SCCAF + 2019-10-20 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf + 0.0.9 + sccaf + 0.0.10 + + + 4 + 3 + 4 + 0 + 4 + 3 + 4 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 110 + 110 + 19 + 19 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 110 + 110 + 19 + 19 + False + + + + sceasy + sceasy_convert + Convert scRNA data object between popular formats + + + + + + + + To update + + Transcriptomics + sceasy + 2019-10-14 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy + 0.0.5 + r-sceasy + 0.0.7 + + 1 + 1 + 1 + 0 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1059 + 1059 + 222 + 222 + 426 + 426 + 71 + 71 + 1 + 1 + 1 + 1 + 1486 + 1486 + 294 + 294 + False @@ -924,7 +3689,7 @@ 1486 294 294 - + False @@ -955,9 +3720,91 @@ 16 16 0 - 16 - 16 - 16 + 16 + 16 + 16 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 16 + 16 + 16 + 0 + 809 + 809 + 78 + 78 + 3 + 3 + 2 + 2 + 105 + 105 + 16 + 16 + 917 + 917 + 96 + 96 + False + + + + scmap + scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features + De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. + + + + + + + + To update + + Transcriptomics, RNA, Statistics, Sequence Analysis + suite_scmap + 2019-08-30 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap + 1.6.4 + scmap-cli + 0.1.0 + + + 0 + 0 + 7 + 0 + 0 + 0 + 7 + 0 + 0 + 0 0 0 0 @@ -981,29 +3828,26 @@ 0 0 0 + 1 0 0 - 16 - 16 - 16 + 97 + 97 + 41 + 41 0 - 809 - 809 - 78 - 78 - 3 - 3 - 2 - 2 - 105 - 105 - 16 - 16 - 917 - 917 - 96 - 96 - + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 97 + 97 + 41 + 41 + False @@ -1082,7 +3926,165 @@ 1419 96 100 + False + + + + scpred + scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model + De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 + + + + + + + + To update + + Transcriptomics, RNA, Statistics, Sequence Analysis + suite_scpred + 2020-04-07 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred + 1.0.2 + scpred-cli + 0.1.0 + + + 0 + 0 + 4 + 0 + 0 + 0 + 4 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 25 + 25 + 5 + 5 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 25 + 25 + 5 + 5 + False + + + + seurat + seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features + De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 + + + + + + + + To update + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ + Transcriptomics, RNA, Statistics, Sequence Analysis + suite_seurat + 2018-07-09 + ebi-gxa + + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat + 4.0.0 + seurat-scripts + 4.4.0 + + 14 + 14 + 14 + 11 + 14 + 14 + 14 + 11 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 19 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 2296 + 2328 + 673 + 676 + 141 + 141 + 39 + 39 + 0 + 0 + 0 + 0 + 2437 + 2469 + 712 + 715 + False @@ -1161,7 +4163,7 @@ 153 16 16 - + False @@ -1240,7 +4242,7 @@ 463 110 110 - + False @@ -1319,7 +4321,7 @@ 1957 20 20 - + False @@ -1398,7 +4400,86 @@ 0 0 0 + False + + + + ucsc-cell-browser + ucsc_cell_browser + Python pipeline and Javascript scatter plot library for single-cell datasets + + + + + + + + To update + https://cells.ucsc.edu/ + Transcriptomics + ucsc_cell_browser + 2018-09-11 + ebi-gxa + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml + https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser + 1.0.0+galaxy1 + ucsc-cell-browser + 1.2.8 + + 0 + 0 + 1 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 0 + 965 + 975 + 178 + 181 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 965 + 975 + 178 + 181 + False @@ -1477,7 +4558,7 @@ 89568 2183 2316 - + False @@ -1556,7 +4637,86 @@ 45 11 11 + False + + + + volcanoplot + volcanoplot + Tool to create a Volcano Plot + + + + + + + To update + https://ggplot2.tidyverse.org/ + Visualization, Transcriptomics, Statistics + volcanoplot + 2018-10-14 + iuc + https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot + https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot + 0.0.6 + r-ggplot2 + 2.2.1 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 0 + 0 + 0 + 1 + 1 + 1 + 0 + 34917 + 36852 + 3670 + 3786 + 54931 + 54931 + 5597 + 5597 + 7183 + 7183 + 905 + 905 + 97031 + 98966 + 10172 + 10288 + False diff --git a/communities/spoc/resources/tools.tsv b/communities/spoc/resources/tools.tsv index cdd045ef..c0645bef 100644 --- a/communities/spoc/resources/tools.tsv +++ b/communities/spoc/resources/tools.tsv @@ -1,19 +1,59 @@ Galaxy wrapper id Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Date of first commit of the suite Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version EDAM operation (no superclasses) EDAM topic (no superclasses) Available on UseGalaxy.org (Main) Available on UseGalaxy.org.au Available on UseGalaxy.eu Available on UseGalaxy.fr Tools available on UseGalaxy.org (Main) Tools available on UseGalaxy.org.au Tools available on UseGalaxy.eu Tools available on UseGalaxy.fr Tools available on APOSTL Tools available on ARGs-OAP Tools available on CIRM-CFBP Tools available on ChemFlow Tools available on Coloc-stats Tools available on CropGalaxy Tools available on Dintor Tools available on GASLINI Tools available on Galaxy@AuBi Tools available on Galaxy@Pasteur Tools available on GalaxyTrakr Tools available on Genomic Hyperbrowser Tools available on GigaGalaxy Tools available on HyPhy HIV NGS Tools Tools available on IPK Galaxy Blast Suite Tools available on ImmPort Galaxy Tools available on InteractoMIX Tools available on MISSISSIPPI Tools available on Mandoiu Lab Tools available on MiModD NacreousMap Tools available on Oqtans Tools available on Palfinder Tools available on PepSimili Tools available on PhagePromotor Tools available on UseGalaxy.be Tools available on UseGalaxy.cz Tools available on UseGalaxy.no Tools available on Viral Variant Visualizer (VVV) No. of tool users (5 years) (usegalaxy.eu) No. of tool users (all time) (usegalaxy.eu) Tool usage (5 years) (usegalaxy.eu) Tool usage (all time) (usegalaxy.eu) No. of tool users (5 years) (usegalaxy.org) No. of tool users (all time) (usegalaxy.org) Tool usage (5 years) (usegalaxy.org) Tool usage (all time) (usegalaxy.org) No. of tool users (5 years) (usegalaxy.org.au) No. of tool users (all time) (usegalaxy.org.au) Tool usage (5 years) (usegalaxy.org.au) Tool usage (all time) (usegalaxy.org.au) No. of tool users (5 years) - all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Single Cell, Spatial Omics anndata 2020-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata 0.10.9 anndata 0.6.22.post1 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 43047 43139 1826 1827 17240 17240 878 878 9309 9309 298 298 69596 69688 3002 3003 False -baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Single Cell, Transcriptomics, Visualization baredsc 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 111 111 8 8 29 29 10 10 21 21 4 4 161 161 22 22 False -cite_seq_count cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens To update https://github.com/Hoohm/CITE-seq-Count Single Cell, Transcriptomics, Proteomics cite_seq_count 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.5 RNA-Seq quantification Transcriptomics, Immunoproteins and antigens 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 4 4 9 9 5 5 18 18 1 1 48 48 10 10 False -cosg cosg Marker gene identification for single-cell sequencing data using COSG. Up-to-date https://github.com/genecell/COSG Transcriptomics, Sequence Analysis, Single Cell cosg 2024-05-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg 1.0.1 cosg 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils 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. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Single Cell, Sequence Analysis dropletutils 2019-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 Sequencing, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4413 4442 430 431 4403 4403 255 255 1816 1816 33 33 10632 10661 718 719 False -episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Single Cell, Epigenetics episcanpy 2023-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy 0.3.2 episcanpy 0.4.0 Enrichment analysis, Imputation Epigenomics, Cell biology, DNA 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 880 880 80 80 221 221 37 37 49 49 3 3 1150 1150 120 120 False -raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Single Cell, Transcriptomics 2021-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid 0.2.3 r-raceid 0.1.3 5 5 5 1 5 5 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3077 4581 395 518 2856 2856 1093 1093 1977 1977 19 19 7910 9414 1507 1630 False -scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy scanpy SCANPY 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. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Single Cell, Spatial Omics, Transcriptomics scanpy 2024-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy 1.10.2 scanpy 1.7.2 Differential gene expression analysis Gene expression, Cell biology, Genetics 6 6 6 0 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 63789 64034 2543 2547 29962 29962 1185 1185 18028 18028 379 379 111779 112024 4107 4111 False -scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Single Cell, Transcriptomics, Visualization 2019-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 Read pre-processing, Sequence visualisation Quality affairs, Molecular genetics 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 1345 1371 350 351 0 0 0 0 903 903 29 29 2248 2274 379 380 False -sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Single Cell, Spatial Omics, Convert Formats sceasy_convert 2023-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy 0.0.7 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 False -schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization, Single Cell schicexplorer 2019-12-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 16 16 16 0 16 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 809 809 78 78 3 3 2 2 105 105 16 16 917 917 96 96 False -scpipe scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, Single Cell scpipe 2018-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 284 632 34 38 786 786 61 61 1 1 1 1 1071 1419 96 100 False -seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics To update https://satijalab.org/seurat/ Single Cell, Transcriptomics, Sequence Analysis seurat 2020-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 5.0 r-seurat 3.0.2 1 1 7 1 1 1 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 121 121 11 11 32 32 5 5 0 0 0 0 153 153 16 16 False -sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools Up-to-date https://github.com/timoast/sinto Single Cell, Epigenetics 2023-04-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto 0.10.1 sinto 0.10.1 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 284 284 70 70 165 165 38 38 14 14 2 2 463 463 110 110 False -snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis To update https://kzhang.org/SnapATAC2/ Single Cell, Epigenetics snapatac2 2024-05-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 2.6.4 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1817 1817 14 14 4 4 2 2 136 136 4 4 1957 1957 20 20 False -spapros spapros_evaluation, spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. Up-to-date https://github.com/theislab/spapros Single Cell, Transcriptomics, Sequence Analysis spapros 2024-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros 0.1.5 spapros 0.1.5 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Up-to-date https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics, Single Cell 2021-07-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.5 umi_tools 1.1.5 Sequencing quality control Sequence sites, features and motifs, Quality affairs 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 5 0 0 0 0 0 0 3 5 5 0 55050 68123 1090 1223 9001 9001 906 906 12444 12444 187 187 76495 89568 2183 2316 False -velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics, Single Cell velocyto 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto 0.17.17 velocyto.py 0.17.17 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 4 4 22 22 6 6 16 16 1 1 45 45 11 11 False +anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Single Cell, Spatial Omics anndata 2020-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata 0.10.9 anndata 0.6.22.post1 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 43047 43139 1826 1827 17240 17240 878 878 9309 9309 298 298 69596 69688 3002 3003 True False True +baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Single Cell, Transcriptomics, Visualization baredsc 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 111 111 8 8 29 29 10 10 21 21 4 4 161 161 22 22 True False True +cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 1.1.1 cell-types-analysis 0.1.11 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 4 4 0 0 0 0 0 0 0 0 8 8 4 4 True False True +cemitool cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Up-to-date https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool 2022-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.26.0 bioconductor-cemitool 1.26.0 Enrichment analysis, Pathway or network analysis Transcriptomics, Microarray experiment 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 225 225 32 32 271 271 61 61 0 0 0 0 496 496 93 93 True False True +cite_seq_count cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens To update https://github.com/Hoohm/CITE-seq-Count Single Cell, Transcriptomics, Proteomics cite_seq_count 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.5 RNA-Seq quantification Transcriptomics, Immunoproteins and antigens 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 4 4 9 9 5 5 18 18 1 1 48 48 10 10 True False True +cosg cosg Marker gene identification for single-cell sequencing data using COSG. Up-to-date https://github.com/genecell/COSG Transcriptomics, Sequence Analysis, Single Cell cosg 2024-05-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg 1.0.1 cosg 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +crosscontamination_barcode_filter crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter 2018-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 276 390 61 76 131 131 42 42 0 0 0 0 407 521 103 118 True False True +data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 441 451 83 87 3 3 2 2 0 0 0 0 444 454 85 89 True False True +data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa v0.0.2+galaxy2 wget 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 867 877 213 216 339 339 94 94 64 64 5 5 1270 1280 312 315 True False True +decoupler score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities To update https://decoupler-py.readthedocs.io/en/latest/ Transcriptomics suite_decoupler 2023-09-24 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler 1.4.0+galaxy3 decoupler 1.5.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 54 6 6 0 0 0 0 0 0 0 0 54 54 6 6 True False True +deg_annotate deg_annotate Annotate DESeq2/DEXSeq output tables To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate Transcriptomics deg_annotate 2018-11-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate 1.1.0 bedtools 2.31.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22774 23146 4084 4155 33972 33972 5372 5372 4236 4236 846 846 60982 61354 10302 10373 True False True +deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 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. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 2018-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 Differential gene expression analysis, RNA-Seq analysis RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 97434 109474 11355 12514 183905 246475 24951 31957 18551 20166 2647 2905 299890 376115 38953 47376 True False True +deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization 2018-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +dexseq dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model 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. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Up-to-date https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.48.0 bioconductor-dexseq 1.48.0 Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 14874 16927 533 837 18475 28854 1403 2568 3854 4271 141 163 37203 50052 2077 3568 True False True +dropletutils dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils 2019-01-22 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils 1.0.4 dropletutils-scripts 0.0.5 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1900 1901 412 413 609 609 131 131 0 0 0 0 2509 2510 543 544 True False True +dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils 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. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Single Cell, Sequence Analysis dropletutils 2019-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 Sequencing, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4413 4442 430 431 4403 4403 255 255 1816 1816 33 33 10632 10661 718 719 True False True +edger edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact 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. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger 2019-02-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger 3.36.0 bioconductor-edger 4.0.16 Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 19294 20905 2423 2618 48876 58723 6341 7527 8010 8705 846 892 76180 88333 9610 11037 True False True +egsea egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea 2018-01-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 Gene set testing Systems biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2809 3060 371 402 5179 5179 759 759 1931 1931 226 226 9919 10170 1356 1387 True False True +episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Single Cell, Epigenetics episcanpy 2023-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy 0.3.2 episcanpy 0.4.0 Enrichment analysis, Imputation Epigenomics, Cell biology, DNA 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 880 880 80 80 221 221 37 37 49 49 3 3 1150 1150 120 120 True False True +fgsea fgsea Perform gene set testing using fgsea fgsea fgsea fgsea 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. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea 2018-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 Gene-set enrichment analysis Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5618 5820 582 607 21673 21673 938 938 869 869 110 110 28160 28362 1630 1655 True False True +garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett 2020-04-03 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett 0.2.8 garnett-cli 0.0.5 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 11 11 0 0 0 0 0 0 0 0 27 27 11 11 True False True +gsc_filter_cells filter_cells Filter single cell RNAseq data on libray depth and number of detected genes To update http://artbio.fr Transcriptomics gsc_filter_cells 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +gsc_filter_genes filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_filter_genes 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +gsc_gene_expression_correlations single_cell_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations To update http://artbio.fr Transcriptomics gsc_gene_expression_correlations 2019-06-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation 2019-07-09 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation 4.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +gsc_mannwhitney_de mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data To update http://artbio.fr Transcriptomics gsc_mannwhitney_de 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de 4.1.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +gsc_scran_normalize scran_normalize Normalize raw counts using scran To update http://artbio.fr Transcriptomics gsc_scran_normalize 2019-09-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize 1.28.1+galaxy0 bioconductor-scran 1.30.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 24 24 3 3 2 2 10 10 2 2 102 102 28 28 True False True +gsc_signature_score signature_score Compute signature scores from single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_signature_score 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score 2.3.9+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +heinz heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz heinz, bionet Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz 2018-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 1281 1434 367 442 1559 1559 636 636 678 678 52 52 3518 3671 1055 1130 True False True +infercnv infercnv Infer Copy Number Variation from Single-Cell RNA-Seq Data Up-to-date https://github.com/broadinstitute/infercnv Transcriptomics, Variant Analysis infercnv 2024-07-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv 1.20.0 bioconductor-infercnv 1.20.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 2 2 0 0 0 0 0 0 0 0 10 10 2 2 True False True +monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 2019-09-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 0.1.4 monocle3-cli 0.0.9 9 0 9 0 9 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3610 3610 559 559 1728 1728 434 434 0 0 0 0 5338 5338 993 993 True False True +multigsea multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea 2023-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 106 106 25 25 0 0 0 0 0 0 0 0 106 106 25 25 True False True +music_deconvolution music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) Up-to-date https://github.com/xuranw/MuSiC Transcriptomics music 2021-09-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution 0.1.1 music-deconvolution 0.1.1 5 5 4 0 5 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2801 2801 289 289 364 364 80 80 1357 1357 21 21 4522 4522 390 390 True False True +pyscenic pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ To update Transcriptomics, RNA, Sequence Analysis suite_pyscenic 2024-08-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic 0.12.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Single Cell, Transcriptomics 2021-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid 0.2.3 r-raceid 0.1.3 5 5 5 1 5 5 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3077 4581 395 518 2856 2856 1093 1093 1977 1977 19 19 7910 9414 1507 1630 True False True +rgrnastar rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper star star STAR Ultrafast universal RNA-seq data aligner Sequence alignment RNA-Seq, Transcriptomics To update https://github.com/alexdobin/STAR Next Gen Mappers, Transcriptomics rgrnastar 2023-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar 2.7.11a star 2.7.11b Sequence alignment RNA-Seq, Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 1 1 1 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 0 438078 473957 10142 10900 325474 403925 15284 18791 49662 53138 1359 1449 813214 931020 26785 31140 True False True +salmon alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics 2019-09-18 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Transcriptomics 2 2 3 1 2 2 3 1 0 0 0 0 0 0 0 0 0 2 1 0 0 1 0 0 0 2 0 0 0 0 0 0 3 3 3 0 73085 77081 2243 2319 90634 122835 3402 4726 13371 15818 513 586 177090 215734 6158 7631 True False True +sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 2018-11-05 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 1.8.0 sc3-scripts 0.0.6 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 10 10 0 0 0 0 0 0 0 0 13 13 10 10 True False True +scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy scanpy SCANPY 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. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Single Cell, Spatial Omics, Transcriptomics scanpy 2024-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy 1.10.2 scanpy 1.7.2 Differential gene expression analysis Gene expression, Cell biology, Genetics 6 6 6 0 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 63789 64034 2543 2547 29962 29962 1185 1185 18028 18028 379 379 111779 112024 4107 4111 True False True +scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts 2020-09-29 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy 1.9.3 scanpy-scripts 1.9.301 27 27 27 0 27 27 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 13 0 45501 45666 4832 4868 7304 7304 1846 1846 3106 3106 457 457 55911 56076 7135 7171 True False True +scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater 2018-10-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater 1.10.0 scater-scripts 0.0.5 1 2 6 0 1 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 381 388 99 100 0 0 0 0 297 297 9 9 678 685 108 109 True False True +scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Single Cell, Transcriptomics, Visualization 2019-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 Read pre-processing, Sequence visualisation Quality affairs, Molecular genetics 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 1345 1371 350 351 0 0 0 0 903 903 29 29 2248 2274 379 380 True False True +sccaf run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out SCCAF: Single Cell Clustering Assessment Framework. To update https://github.com/sccaf/sccaf Transcriptomics SCCAF 2019-10-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf 0.0.9 sccaf 0.0.10 4 3 4 0 4 3 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 110 110 19 19 0 0 0 0 0 0 0 0 110 110 19 19 True False True +sceasy sceasy_convert Convert scRNA data object between popular formats To update Transcriptomics sceasy 2019-10-14 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy 0.0.5 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 True False True +sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Single Cell, Spatial Omics, Convert Formats sceasy_convert 2023-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy 0.0.7 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 True False True +schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization, Single Cell schicexplorer 2019-12-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 16 16 16 0 16 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 809 809 78 78 3 3 2 2 105 105 16 16 917 917 96 96 True False True +scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap 2019-08-30 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap 1.6.4 scmap-cli 0.1.0 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 97 97 41 41 0 0 0 0 0 0 0 0 97 97 41 41 True False True +scpipe scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, Single Cell scpipe 2018-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 284 632 34 38 786 786 61 61 1 1 1 1 1071 1419 96 100 True False True +scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred 1.0.2 scpred-cli 0.1.0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 5 5 0 0 0 0 0 0 0 0 25 25 5 5 True False True +seurat seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat 2018-07-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 4.0.0 seurat-scripts 4.4.0 14 14 14 11 14 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 0 0 2296 2328 673 676 141 141 39 39 0 0 0 0 2437 2469 712 715 True False True +seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics To update https://satijalab.org/seurat/ Single Cell, Transcriptomics, Sequence Analysis seurat 2020-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 5.0 r-seurat 3.0.2 1 1 7 1 1 1 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 121 121 11 11 32 32 5 5 0 0 0 0 153 153 16 16 True False True +sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools Up-to-date https://github.com/timoast/sinto Single Cell, Epigenetics 2023-04-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto 0.10.1 sinto 0.10.1 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 284 284 70 70 165 165 38 38 14 14 2 2 463 463 110 110 True False True +snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis To update https://kzhang.org/SnapATAC2/ Single Cell, Epigenetics snapatac2 2024-05-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 2.6.4 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1817 1817 14 14 4 4 2 2 136 136 4 4 1957 1957 20 20 True False True +spapros spapros_evaluation, spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. Up-to-date https://github.com/theislab/spapros Single Cell, Transcriptomics, Sequence Analysis spapros 2024-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros 0.1.5 spapros 0.1.5 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +ucsc-cell-browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser 2018-09-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser 1.0.0+galaxy1 ucsc-cell-browser 1.2.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 965 975 178 181 0 0 0 0 0 0 0 0 965 975 178 181 True False True +umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Up-to-date https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics, Single Cell 2021-07-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.5 umi_tools 1.1.5 Sequencing quality control Sequence sites, features and motifs, Quality affairs 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 5 0 0 0 0 0 0 3 5 5 0 55050 68123 1090 1223 9001 9001 906 906 12444 12444 187 187 76495 89568 2183 2316 True False True +velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics, Single Cell velocyto 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto 0.17.17 velocyto.py 0.17.17 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 4 4 22 22 6 6 16 16 1 1 45 45 11 11 True False True +volcanoplot volcanoplot Tool to create a Volcano Plot To update https://ggplot2.tidyverse.org/ Visualization, Transcriptomics, Statistics volcanoplot 2018-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 0.0.6 r-ggplot2 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 34917 36852 3670 3786 54931 54931 5597 5597 7183 7183 905 905 97031 98966 10172 10288 True False True diff --git a/communities/spoc/resources/tools_filtered_by_ts_categories.tsv b/communities/spoc/resources/tools_filtered_by_ts_categories.tsv index cdd045ef..0564adfb 100644 --- a/communities/spoc/resources/tools_filtered_by_ts_categories.tsv +++ b/communities/spoc/resources/tools_filtered_by_ts_categories.tsv @@ -1,19 +1,106 @@ Galaxy wrapper id Galaxy tool ids Description bio.tool id bio.tool ids biii bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Date of first commit of the suite Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper parsed folder Galaxy wrapper version Conda id Conda version EDAM operation (no superclasses) EDAM topic (no superclasses) Available on UseGalaxy.org (Main) Available on UseGalaxy.org.au Available on UseGalaxy.eu Available on UseGalaxy.fr Tools available on UseGalaxy.org (Main) Tools available on UseGalaxy.org.au Tools available on UseGalaxy.eu Tools available on UseGalaxy.fr Tools available on APOSTL Tools available on ARGs-OAP Tools available on CIRM-CFBP Tools available on ChemFlow Tools available on Coloc-stats Tools available on CropGalaxy Tools available on Dintor Tools available on GASLINI Tools available on Galaxy@AuBi Tools available on Galaxy@Pasteur Tools available on GalaxyTrakr Tools available on Genomic Hyperbrowser Tools available on GigaGalaxy Tools available on HyPhy HIV NGS Tools Tools available on IPK Galaxy Blast Suite Tools available on ImmPort Galaxy Tools available on InteractoMIX Tools available on MISSISSIPPI Tools available on Mandoiu Lab Tools available on MiModD NacreousMap Tools available on Oqtans Tools available on Palfinder Tools available on PepSimili Tools available on PhagePromotor Tools available on UseGalaxy.be Tools available on UseGalaxy.cz Tools available on UseGalaxy.no Tools available on Viral Variant Visualizer (VVV) No. of tool users (5 years) (usegalaxy.eu) No. of tool users (all time) (usegalaxy.eu) Tool usage (5 years) (usegalaxy.eu) Tool usage (all time) (usegalaxy.eu) No. of tool users (5 years) (usegalaxy.org) No. of tool users (all time) (usegalaxy.org) Tool usage (5 years) (usegalaxy.org) Tool usage (all time) (usegalaxy.org) No. of tool users (5 years) (usegalaxy.org.au) No. of tool users (all time) (usegalaxy.org.au) Tool usage (5 years) (usegalaxy.org.au) Tool usage (all time) (usegalaxy.org.au) No. of tool users (5 years) - all main servers No. of tool users (all time) - all main servers Tool usage (5 years) - all main servers Tool usage (all time) - all main servers Reviewed Deprecated To keep -anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Single Cell, Spatial Omics anndata 2020-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata 0.10.9 anndata 0.6.22.post1 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 43047 43139 1826 1827 17240 17240 878 878 9309 9309 298 298 69596 69688 3002 3003 False -baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Single Cell, Transcriptomics, Visualization baredsc 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 111 111 8 8 29 29 10 10 21 21 4 4 161 161 22 22 False -cite_seq_count cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens To update https://github.com/Hoohm/CITE-seq-Count Single Cell, Transcriptomics, Proteomics cite_seq_count 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.5 RNA-Seq quantification Transcriptomics, Immunoproteins and antigens 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 4 4 9 9 5 5 18 18 1 1 48 48 10 10 False -cosg cosg Marker gene identification for single-cell sequencing data using COSG. Up-to-date https://github.com/genecell/COSG Transcriptomics, Sequence Analysis, Single Cell cosg 2024-05-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg 1.0.1 cosg 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils 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. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Single Cell, Sequence Analysis dropletutils 2019-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 Sequencing, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4413 4442 430 431 4403 4403 255 255 1816 1816 33 33 10632 10661 718 719 False -episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Single Cell, Epigenetics episcanpy 2023-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy 0.3.2 episcanpy 0.4.0 Enrichment analysis, Imputation Epigenomics, Cell biology, DNA 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 880 880 80 80 221 221 37 37 49 49 3 3 1150 1150 120 120 False -raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Single Cell, Transcriptomics 2021-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid 0.2.3 r-raceid 0.1.3 5 5 5 1 5 5 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3077 4581 395 518 2856 2856 1093 1093 1977 1977 19 19 7910 9414 1507 1630 False -scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy scanpy SCANPY 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. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Single Cell, Spatial Omics, Transcriptomics scanpy 2024-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy 1.10.2 scanpy 1.7.2 Differential gene expression analysis Gene expression, Cell biology, Genetics 6 6 6 0 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 63789 64034 2543 2547 29962 29962 1185 1185 18028 18028 379 379 111779 112024 4107 4111 False -scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Single Cell, Transcriptomics, Visualization 2019-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 Read pre-processing, Sequence visualisation Quality affairs, Molecular genetics 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 1345 1371 350 351 0 0 0 0 903 903 29 29 2248 2274 379 380 False -sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Single Cell, Spatial Omics, Convert Formats sceasy_convert 2023-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy 0.0.7 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 False -schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization, Single Cell schicexplorer 2019-12-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 16 16 16 0 16 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 809 809 78 78 3 3 2 2 105 105 16 16 917 917 96 96 False -scpipe scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, Single Cell scpipe 2018-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 284 632 34 38 786 786 61 61 1 1 1 1 1071 1419 96 100 False -seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics To update https://satijalab.org/seurat/ Single Cell, Transcriptomics, Sequence Analysis seurat 2020-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 5.0 r-seurat 3.0.2 1 1 7 1 1 1 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 121 121 11 11 32 32 5 5 0 0 0 0 153 153 16 16 False -sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools Up-to-date https://github.com/timoast/sinto Single Cell, Epigenetics 2023-04-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto 0.10.1 sinto 0.10.1 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 284 284 70 70 165 165 38 38 14 14 2 2 463 463 110 110 False -snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis To update https://kzhang.org/SnapATAC2/ Single Cell, Epigenetics snapatac2 2024-05-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 2.6.4 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1817 1817 14 14 4 4 2 2 136 136 4 4 1957 1957 20 20 False -spapros spapros_evaluation, spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. Up-to-date https://github.com/theislab/spapros Single Cell, Transcriptomics, Sequence Analysis spapros 2024-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros 0.1.5 spapros 0.1.5 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 False -umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Up-to-date https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics, Single Cell 2021-07-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.5 umi_tools 1.1.5 Sequencing quality control Sequence sites, features and motifs, Quality affairs 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 5 0 0 0 0 0 0 3 5 5 0 55050 68123 1090 1223 9001 9001 906 906 12444 12444 187 187 76495 89568 2183 2316 False -velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics, Single Cell velocyto 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto 0.17.17 velocyto.py 0.17.17 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 4 4 22 22 6 6 16 16 1 1 45 45 11 11 False +aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers gaeval gaeval GAEVAL Gene Annotation EVAluation. Sequence annotation Sequence analysis, Gene structure Up-to-date https://github.com/BrendelGroup/AEGeAn Transcriptomics, Sequence Analysis aegean 2021-01-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean 0.16.0 aegean 0.16.0 Sequence annotation Sequence analysis, Gene structure 1 4 4 4 1 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0 0 200 200 77 77 83 83 39 39 1747 1747 44 44 2030 2030 160 160 True False False +anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects To update https://anndata.readthedocs.io Single Cell, Spatial Omics anndata 2020-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata 0.10.9 anndata 0.6.22.post1 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 43047 43139 1826 1827 17240 17240 878 878 9309 9309 298 298 69596 69688 3002 3003 True False True +arriba arriba, arriba_draw_fusions, arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR Up-to-date https://github.com/suhrig/arriba Sequence Analysis, Transcriptomics arriba 2022-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba 2.4.0 arriba 2.4.0 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 3670 3670 71 71 3 3 2 2 234 234 10 10 3907 3907 83 83 True False False +askor askor_de AskoR links EdgeR and AskOmics To update https://github.com/askomics/askoR Transcriptomics askor_de 2018-04-09 genouest https://github.com/genouest/galaxy-tools/tree/master/tools/askor https://github.com/genouest/galaxy-tools/tree/master/tools/askor 0.2 bioconductor-limma 3.58.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False +bamparse bamparse Generates hit count lists from bam alignments. To update http://artbio.fr RNA, Transcriptomics bamparse 2017-10-12 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse 4.1.1 pysam 0.22.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False +baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability Up-to-date https://github.com/lldelisle/baredSC Single Cell, Transcriptomics, Visualization baredsc 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc 1.1.3 baredsc 1.1.3 Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 111 111 8 8 29 29 10 10 21 21 4 4 161 161 22 22 True False True +bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 Up-to-date https://github.com/dmaticzka/bctools Sequence Analysis, Transcriptomics 2017-10-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools 0.2.2 bctools 0.2.2 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 7 0 2352 3092 234 265 0 0 0 0 0 0 0 0 2352 3092 234 265 True False False +brew3r_r brew3r_r Extend 3' end of a GTF using another GTF as a template brew3r.r brew3r.r BREW3R.r This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids. Genome annotation Transcriptomics, Genomics To update https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html Transcriptomics, RNA brew3r_r 2024-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r 1.0.2 Genome annotation Transcriptomics 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 6 6 2 2 0 0 0 0 7 7 3 3 True False False +cell-types-analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis To update Transcriptomics, RNA, Statistics suite_cell_types_analysis 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 1.1.1 cell-types-analysis 0.1.11 0 0 6 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 4 4 0 0 0 0 0 0 0 0 8 8 4 4 True False True +cemitool cemitool Gene co-expression network analysis tool cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Up-to-date https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html Transcriptomics, RNA, Statistics cemitool 2022-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool 1.26.0 bioconductor-cemitool 1.26.0 Enrichment analysis, Pathway or network analysis Transcriptomics, Microarray experiment 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 225 225 32 32 271 271 61 61 0 0 0 0 496 496 93 93 True False True +cherri cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions cherri cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. Molecular interactions, pathways and networks, Structure analysis, Machine learning To update https://github.com/BackofenLab/Cherri Transcriptomics, RNA 2022-12-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri 0.7 cherri 0.8 Molecular interactions, pathways and networks, Structure analysis, Machine learning 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 207 207 1 1 0 0 0 0 0 0 0 0 207 207 1 1 True False False +chira chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data chira chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Up-to-date https://github.com/pavanvidem/chira RNA, Transcriptomics, Sequence Analysis chira 2020-01-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira 1.4.3 chira 1.4.3 Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA 5 5 5 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 16542 16542 287 287 1061 1061 102 102 27 27 5 5 17630 17630 394 394 True False False +cite_seq_count cite_seq_count Count CMO/HTO CITE-seq-Count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. RNA-Seq quantification Transcriptomics, Immunoproteins and antigens To update https://github.com/Hoohm/CITE-seq-Count Single Cell, Transcriptomics, Proteomics cite_seq_count 2023-01-18 iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count 1.4.4 cite-seq-count 1.4.5 RNA-Seq quantification Transcriptomics, Immunoproteins and antigens 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 21 21 4 4 9 9 5 5 18 18 1 1 48 48 10 10 True False True +cosg cosg Marker gene identification for single-cell sequencing data using COSG. Up-to-date https://github.com/genecell/COSG Transcriptomics, Sequence Analysis, Single Cell cosg 2024-05-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg 1.0.1 cosg 1.0.1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +cpat cpat Coding-potential assessment tool using an alignment-free logistic regression model. Up-to-date https://github.com/liguowang/cpat Transcriptomics cpat 2023-02-01 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cpat https://github.com/bgruening/galaxytools/tree/master/tools/cpat 3.0.5 cpat 3.0.5 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 204 204 47 47 165 165 40 40 125 125 7 7 494 494 94 94 True False False +cpm_tpm_rpk cpm_tpm_rpk Generate CPM,TPM or RPK from raw counts To update http://artbio.fr Transcriptomics cpm_tpm_rpk 2018-07-13 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk 0.6.0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False +crosscontamination_barcode_filter crosscontamination_barcode_filter Barcode contamination discovery tool To update Transcriptomics, Visualization crosscontamination_barcode_filter 2018-07-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter 0.3 r-ggplot2 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 276 390 61 76 131 131 42 42 0 0 0 0 407 521 103 118 True False True +cuffcompare cuffcompare Galaxy wrappers for the Cuffcompare tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffcompare 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 768 1199 171 300 2205 24981 754 5750 251 493 46 98 3224 26673 971 6148 True False False +cuffdiff cuffdiff Galaxy wrappers for the Cuffdiff tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffdiff 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff 2.2.1 cufflinks 2.2.1 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 4176 6065 564 725 24284 117007 4952 20249 971 4231 193 616 29431 127303 5709 21590 True False False +cufflinks cufflinks Galaxy wrappers for the Cufflinks tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cufflinks 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 1 0 0 0 1 1 1 0 26122 33320 870 1213 70653 349091 6984 27076 3963 10315 440 836 100738 392726 8294 29125 True False False +cuffmerge cuffmerge Galaxy wrappers for the Cuffmerge tool. Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffmerge 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge 2.2.1 cufflinks 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 2406 3448 351 637 20978 67769 3641 13764 1209 3057 227 573 24593 74274 4219 14974 True False False +cuffnorm cuffnorm The Cuffnorm tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffnorm 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm 2.2.1 cufflinks 2.2.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 374 701 81 114 1032 13499 273 1166 262 322 53 70 1668 14522 407 1350 True False False +cuffquant cuffquant The Cuffquant tool Up-to-date http://cole-trapnell-lab.github.io/cufflinks/ Transcriptomics cuffquant 2020-06-08 devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant 2.2.1 cufflinks 2.2.1 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 408 732 54 71 1964 15883 267 1310 308 422 26 46 2680 17037 347 1427 True False False +data-hca hca_matrix_downloader Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects To update Transcriptomics, Sequence Analysis suite_human_cell_atlas_tools 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca v0.0.4+galaxy0 hca-matrix-downloader 0.0.4 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 441 451 83 87 3 3 2 2 0 0 0 0 444 454 85 89 True False True +data-scxa retrieve_scxa Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home To update Transcriptomics, Sequence Analysis suite_ebi_expression_atlas 2019-07-02 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa v0.0.2+galaxy2 wget 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 867 877 213 216 339 339 94 94 64 64 5 5 1270 1280 312 315 True False True +decoupler score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities To update https://decoupler-py.readthedocs.io/en/latest/ Transcriptomics suite_decoupler 2023-09-24 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler 1.4.0+galaxy3 decoupler 1.5.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 54 6 6 0 0 0 0 0 0 0 0 54 54 6 6 True False True +deg_annotate deg_annotate Annotate DESeq2/DEXSeq output tables To update https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate Transcriptomics deg_annotate 2018-11-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate 1.1.0 bedtools 2.31.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 22774 23146 4084 4155 33972 33972 5372 5372 4236 4236 846 846 60982 61354 10302 10373 True False True +deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution DESeq2 DESeq2 DESeq2 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. Differential gene expression analysis, RNA-Seq analysis RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics deseq2 2018-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 2.11.40.8 bioconductor-deseq2 1.42.0 Differential gene expression analysis, RNA-Seq analysis RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 97434 109474 11355 12514 183905 246475 24951 31957 18551 20166 2647 2905 299890 376115 38953 47376 True False True +deseq2_normalization deseq2_normalization Normalizes gene hitlists To update http://artbio.fr RNA, Transcriptomics, Sequence Analysis, Statistics deseq2_normalization 2018-01-05 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization 1.40.2+galaxy0 bioconductor-deseq2 1.42.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +dexseq dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model 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. Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq Up-to-date https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html Transcriptomics, RNA, Statistics dexseq 2018-05-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq 1.48.0 bioconductor-dexseq 1.48.0 Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq 3 3 3 3 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 14874 16927 533 837 18475 28854 1403 2568 3854 4271 141 163 37203 50052 2077 3568 True False True +dropletutils dropletutils_empty_drops, dropletutils_read_10x De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_dropletutils 2019-01-22 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils 1.0.4 dropletutils-scripts 0.0.5 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1900 1901 412 413 609 609 131 131 0 0 0 0 2509 2510 543 544 True False True +dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data dropletutils dropletutils DropletUtils 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. Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics To update https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html Single Cell, Sequence Analysis dropletutils 2019-09-02 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils 1.10.0 bioconductor-dropletutils 1.22.0 Sequencing, Transcriptomics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4413 4442 430 431 4403 4403 255 255 1816 1816 33 33 10632 10661 718 719 True False True +edger edger Perform RNA-Seq differential expression analysis using edgeR pipeline edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact 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. Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq To update http://bioconductor.org/packages/release/bioc/html/edgeR.html Transcriptomics, RNA, Statistics edger 2019-02-08 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger 3.36.0 bioconductor-edger 4.0.16 Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 19294 20905 2423 2618 48876 58723 6341 7527 8010 8705 846 892 76180 88333 9610 11037 True False True +egsea egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. Gene set testing Systems biology To update https://bioconductor.org/packages/release/bioc/html/EGSEA.html Transcriptomics, RNA, Statistics egsea 2018-01-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea 1.20.0 bioconductor-egsea 1.28.0 Gene set testing Systems biology 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2809 3060 371 402 5179 5179 759 759 1931 1931 226 226 9919 10170 1356 1387 True False True +episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. Enrichment analysis, Imputation Epigenomics, Cell biology, DNA To update https://github.com/colomemaria/epiScanpy Single Cell, Epigenetics episcanpy 2023-03-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy 0.3.2 episcanpy 0.4.0 Enrichment analysis, Imputation Epigenomics, Cell biology, DNA 3 3 3 0 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 880 880 80 80 221 221 37 37 49 49 3 3 1150 1150 120 120 True False True +fastq_provider fastq_provider Retrieval and download of FASTQ files from ENA and other repositories such as HCA. To update https://github.com/ebi-gene-expression-group/atlas-fastq-provider Data Source, RNA, Transcriptomics atlas_fastq_provider 2022-03-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider 0.4.4 atlas-fastq-provider 0.4.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False +fastq_utils fastq_filter_n, fastq_trim_poly_at Set of tools for handling fastq files To update https://github.com/nunofonseca/fastq_utils Transcriptomics, RNA fastq_utils 2022-02-15 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils 0.25.1+galaxy0 fastq_utils 0.25.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False +featurecounts featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. Read summarisation, RNA-Seq quantification RNA-Seq To update http://bioinf.wehi.edu.au/featureCounts RNA, Transcriptomics, Sequence Analysis featurecounts 2019-05-28 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts 2.0.3 subread 2.0.6 Read summarisation, RNA-Seq quantification RNA-Seq 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 0 740719 770524 11699 12547 643892 784396 23272 27598 66108 68867 2348 2463 1450719 1623787 37319 42608 True False False +fgsea fgsea Perform gene set testing using fgsea fgsea fgsea fgsea 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. Gene-set enrichment analysis Genetics To update https://bioconductor.org/packages/release/bioc/html/fgsea.html Visualization, Transcriptomics, Statistics fgsea 2018-10-19 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 Gene-set enrichment analysis Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5618 5820 582 607 21673 21673 938 938 869 869 110 110 28160 28362 1630 1655 True False True +garnett garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_garnett 2020-04-03 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett 0.2.8 garnett-cli 0.0.5 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 27 11 11 0 0 0 0 0 0 0 0 27 27 11 11 True False True +genomic_super_signature genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases genomicsupersignature genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment To update https://github.com/shbrief/GenomicSuperSignature Sequence Analysis, RNA, Transcriptomics genomic_super_signature 2022-01-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature 1.2.0 bioconductor-genomicsupersignature 1.10.0 Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 47 47 13 13 0 0 0 0 0 0 0 0 47 47 13 13 True False False +gffcompare gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. gffcompare gffcompare gffcompare Program for comparing, annotating, merging and tracking transcripts in GFF files. Sequence annotation Nucleic acids, Sequence analysis Up-to-date https://github.com/gpertea/gffcompare/ Transcriptomics gffcompare 2018-10-29 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare 0.12.6 gffcompare 0.12.6 Sequence annotation Nucleic acids, Sequence analysis 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3560 3980 916 999 5281 8000 1713 2521 1468 1642 208 225 10309 13622 2837 3745 True False False +gsc_filter_cells filter_cells Filter single cell RNAseq data on libray depth and number of detected genes To update http://artbio.fr Transcriptomics gsc_filter_cells 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +gsc_filter_genes filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_filter_genes 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +gsc_gene_expression_correlations single_cell_gene_expression_correlations Compute single-cell paire-wise gene expressions correlations To update http://artbio.fr Transcriptomics gsc_gene_expression_correlations 2019-06-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations 4.3.1+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +gsc_high_dimensions_visualisation high_dimensions_visualisation Generates PCA, t-SNE and HCPC visualisation To update http://artbio.fr Transcriptomics, Visualization gsc_high_dimensions_visualisation 2019-07-09 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation 4.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +gsc_mannwhitney_de mannwhitney_de Perform a mann-whitney differential testing between two sets of gene expression data To update http://artbio.fr Transcriptomics gsc_mannwhitney_de 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de 4.1.3+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +gsc_scran_normalize scran_normalize Normalize raw counts using scran To update http://artbio.fr Transcriptomics gsc_scran_normalize 2019-09-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize 1.28.1+galaxy0 bioconductor-scran 1.30.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 89 89 24 24 3 3 2 2 10 10 2 2 102 102 28 28 True False True +gsc_signature_score signature_score Compute signature scores from single cell RNAseq data To update http://artbio.fr Transcriptomics gsc_signature_score 2019-06-23 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score 2.3.9+galaxy0 r-optparse 1.3.2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +heinz heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. heinz heinz, bionet Heinz Tool for single-species active module discovery. Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks To update https://github.com/ls-cwi/heinz Transcriptomics, Visualization, Statistics heinz 2018-06-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz 1.0 bioconductor-bionet 1.62.0 Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 1281 1434 367 442 1559 1559 636 636 678 678 52 52 3518 3671 1055 1130 True False True +infercnv infercnv Infer Copy Number Variation from Single-Cell RNA-Seq Data Up-to-date https://github.com/broadinstitute/infercnv Transcriptomics, Variant Analysis infercnv 2024-07-23 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv 1.20.0 bioconductor-infercnv 1.20.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 2 2 0 0 0 0 0 0 0 0 10 10 2 2 True False True +isoformswitchanalyzer isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR 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. Sequence comparison, Sequence analysis Computational biology, Gene transcripts To update https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html Transcriptomics, RNA, Statistics isoformswitchanalyzer 2023-05-24 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 Sequence comparison, Sequence analysis Computational biology, Gene transcripts 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1301 1301 59 59 1331 1331 60 60 507 507 9 9 3139 3139 128 128 True False False +kallisto kallisto_pseudo, kallisto_quant kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. kallisto kallisto kallisto A program for quantifying abundances of transcripts from RNA-Seq data, 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. Gene expression profiling Transcriptomics, RNA-seq, Gene expression To update https://pachterlab.github.io/kallisto/ Transcriptomics 2017-08-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto 0.48.0 kallisto 0.51.1 Gene expression profiling Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 28398 29031 932 965 73705 80087 2603 3025 5333 5567 218 230 107436 114685 3753 4220 True False False +limma_voom limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline limma limma limma Data analysis, linear models and differential expression for microarray data. RNA-Seq analysis Molecular biology, Genetics Up-to-date http://bioconductor.org/packages/release/bioc/html/limma.html Transcriptomics, RNA, Statistics limma_voom 2019-02-17 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom 3.58.1 bioconductor-limma 3.58.1 RNA-Seq analysis Molecular biology, Genetics 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 23442 24466 2379 2475 45734 49342 4565 5032 9327 9517 835 842 78503 83325 7779 8349 True False False +masigpro masigpro Identify significantly differential expression profiles in time-course microarray experiments masigpro masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics masigpro 2017-05-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro 1.49.3 coreutils 8.25 Regression analysis Gene expression, Microarray experiment, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 471 582 35 40 589 589 80 80 0 0 0 0 1060 1171 115 120 True False False +mircounts mircounts Generates miRNA count lists from read alignments to mirBase. To update http://artbio.fr RNA, Transcriptomics mircounts 2017-07-24 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts 1.6 tar 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1458 1458 36 36 1458 1458 36 36 True False False +monocle3 monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_monocle3 2019-09-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3 0.1.4 monocle3-cli 0.0.9 9 0 9 0 9 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3610 3610 559 559 1728 1728 434 434 0 0 0 0 5338 5338 993 993 True False True +multigsea multigsea GSEA-based pathway enrichment analysis for multi-omics data multiGSEA multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Up-to-date https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html Transcriptomics, Proteomics, Statistics multigsea 2023-06-07 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea 1.12.0 bioconductor-multigsea 1.12.0 Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 106 106 25 25 0 0 0 0 0 0 0 0 106 106 25 25 True False True +music_deconvolution music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) Up-to-date https://github.com/xuranw/MuSiC Transcriptomics music 2021-09-12 bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution 0.1.1 music-deconvolution 0.1.1 5 5 4 0 5 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2801 2801 289 289 364 364 80 80 1357 1357 21 21 4522 4522 390 390 True False True +nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. Duplication detection Sequencing Up-to-date https://github.com/tecangenomics/nudup SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup 2016-11-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup 2.3.3 nudup 2.3.3 Duplication detection Sequencing 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False +pathifier pathifier pathifier Up-to-date https:// Transcriptomics, Statistics pathifier 2019-11-08 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier 1.40.0 bioconductor-pathifier 1.40.0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 245 245 10 10 0 0 0 0 0 0 0 0 245 245 10 10 True False False +pizzly pizzly Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. To update https://github.com/pmelsted/pizzly/ Transcriptomics 2017-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly 0.37.3.1 pizzly 0.37.3 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 201 210 23 24 998 998 76 76 0 0 0 0 1199 1208 99 100 True False False +psiclass psiclass PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. psiclass psiclass PsiCLASS Reference-based transcriptome assembler for single or multiple RNA-seq samples Transcriptome assembly Sequence assembly Up-to-date https://github.com/splicebox/PsiCLASS Transcriptomics psiclass 2023-09-06 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass 1.0.3 psiclass 1.0.3 Transcriptome assembly Sequence assembly 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 24 24 5 5 0 0 0 0 0 0 0 0 24 24 5 5 True False False +pyscenic pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/ To update Transcriptomics, RNA, Sequence Analysis suite_pyscenic 2024-08-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic 0.12.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. qualimap qualimap QualiMap 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. Sequencing quality control Data quality management Up-to-date http://qualimap.bioinfo.cipf.es/ Sequence Analysis, Transcriptomics, SAM qualimap 2019-10-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap 2.3 qualimap 2.3 Sequencing quality control Data quality management 4 4 4 1 4 4 4 1 0 0 0 0 0 0 0 0 0 0 4 0 0 1 0 0 0 1 0 0 0 0 0 0 4 4 4 0 684820 684820 3239 3239 90503 90503 3881 3881 29018 29018 826 826 804341 804341 7946 7946 True False False +raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis To update https://github.com/dgrun/RaceID3_StemID2_package/ Single Cell, Transcriptomics 2021-04-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid 0.2.3 r-raceid 0.1.3 5 5 5 1 5 5 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 3077 4581 395 518 2856 2856 1093 1093 1977 1977 19 19 7910 9414 1507 1630 True False True +repenrich edger-repenrich, repenrich Repeat element profiling To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich Transcriptomics repenrich 2017-05-31 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich 2.31.1 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1725 1790 56 57 1725 1790 56 57 True False False +repenrich2 edger-repenrich2, repenrich2 Repeat element profiling using bowtie2 aligner To update https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 Transcriptomics repenrich2 2024-04-20 artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 2.31.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False +rgrnastar rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper star star STAR Ultrafast universal RNA-seq data aligner Sequence alignment RNA-Seq, Transcriptomics To update https://github.com/alexdobin/STAR Next Gen Mappers, Transcriptomics rgrnastar 2023-02-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar 2.7.11a star 2.7.11b Sequence alignment RNA-Seq, Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 1 1 1 0 0 2 0 0 0 2 0 0 0 0 0 0 2 2 2 0 438078 473957 10142 10900 325474 403925 15284 18791 49662 53138 1359 1449 813214 931020 26785 31140 True False True +ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Computational biology To update https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA 2022-09-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz 1.2.0 ribowaltz 2.0 Computational biology 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 171 171 20 20 0 0 0 0 0 0 0 0 171 171 20 20 True False False +rsem extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie transcript quantification from RNA-Seq data To update https://github.com/deweylab/RSEM Transcriptomics, RNA rsem 2018-03-28 artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem rsem 1.3.3 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 1 1 0 363 430 158 183 0 0 0 0 67 146 13 39 430 576 171 222 True False False +rseqc rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin an RNA-seq quality control package rseqc rseqc RSeQC 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. Data handling Sequencing To update https://code.google.com/p/rseqc/ Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization rseqc 2017-02-27 nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc 5.0.3 rseqc 5.0.4 Data handling Sequencing 22 22 22 22 22 22 22 22 0 0 0 0 0 0 0 0 22 0 0 0 0 22 0 0 0 22 0 0 0 0 0 0 22 22 22 0 136315 147595 8341 9385 138707 161046 10696 12789 22718 23767 1593 1695 297740 332408 20630 23869 True False False +ruvseq ruvseq Remove Unwanted Variation from RNA-Seq Data ruvseq ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. Differential gene expression analysis Gene expression, RNA-seq To update https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Transcriptomics, RNA, Statistics ruvseq 2018-08-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq 1.26.0 bioconductor-ruvseq 1.36.0 Differential gene expression analysis Gene expression 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1286 1364 178 193 2220 2220 299 299 0 0 0 0 3506 3584 477 492 True False False +salmon alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics 2019-09-18 bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Transcriptomics 2 2 3 1 2 2 3 1 0 0 0 0 0 0 0 0 0 2 1 0 0 1 0 0 0 2 0 0 0 0 0 0 3 3 3 0 73085 77081 2243 2319 90634 122835 3402 4726 13371 15818 513 586 177090 215734 6158 7631 True False True +sashimi_plot sashimi_plot Generates a sashimi plot from bam files. To update http://artbio.fr RNA, Transcriptomics, Graphics, Visualization sashimi_plot 2019-08-21 artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot 0.1.1 python 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False False +sc3 sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_sc3 2018-11-05 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3 1.8.0 sc3-scripts 0.0.6 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 10 10 0 0 0 0 0 0 0 0 13 13 10 10 True False True +scanpy anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. To update https://scanpy.readthedocs.io Transcriptomics, Sequence Analysis, RNA scanpy_scripts 2020-09-29 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy 1.9.3 scanpy-scripts 1.9.301 27 27 27 0 27 27 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 13 0 45501 45666 4832 4868 7304 7304 1846 1846 3106 3106 457 457 55911 56076 7135 7171 True False True +scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders Scanpy – Single-Cell Analysis in Python scanpy scanpy SCANPY 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. Differential gene expression analysis Gene expression, Cell biology, Genetics To update https://scanpy.readthedocs.io Single Cell, Spatial Omics, Transcriptomics scanpy 2024-09-03 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy 1.10.2 scanpy 1.7.2 Differential gene expression analysis Gene expression, Cell biology, Genetics 6 6 6 0 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 63789 64034 2543 2547 29962 29962 1185 1185 18028 18028 379 379 111779 112024 4107 4111 True False True +scater scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scater 2018-10-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater 1.10.0 scater-scripts 0.0.5 1 2 6 0 1 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 381 388 99 100 0 0 0 0 297 297 9 9 678 685 108 109 True False True +scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. Read pre-processing, Sequencing quality control, Sequence visualisation RNA-seq, Quality affairs, Molecular genetics To update http://bioconductor.org/packages/scater/ Single Cell, Transcriptomics, Visualization 2019-07-18 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater 1.22.0 bioconductor-scater 1.30.1 Read pre-processing, Sequence visualisation Quality affairs, Molecular genetics 0 5 5 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 1345 1371 350 351 0 0 0 0 903 903 29 29 2248 2274 379 380 True False True +sccaf run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out SCCAF: Single Cell Clustering Assessment Framework. To update https://github.com/sccaf/sccaf Transcriptomics SCCAF 2019-10-20 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf 0.0.9 sccaf 0.0.10 4 3 4 0 4 3 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 110 110 19 19 0 0 0 0 0 0 0 0 110 110 19 19 True False True +sceasy sceasy_convert Convert scRNA data object between popular formats To update Transcriptomics sceasy 2019-10-14 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy 0.0.5 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 True False True +sceasy sceasy_convert Converter between difference single-cell formats Up-to-date https://github.com/cellgeni/sceasy/ Single Cell, Spatial Omics, Convert Formats sceasy_convert 2023-11-10 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy 0.0.7 r-sceasy 0.0.7 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1059 1059 222 222 426 426 71 71 1 1 1 1 1486 1486 294 294 True False True +schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. To update https://github.com/joachimwolff/schicexplorer Sequence Analysis, Transcriptomics, Visualization, Single Cell schicexplorer 2019-12-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 4 schicexplorer 7 16 16 16 0 16 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 809 809 78 78 3 3 2 2 105 105 16 16 917 917 96 96 True False True +scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap 2019-08-30 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap 1.6.4 scmap-cli 0.1.0 0 0 7 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 97 97 41 41 0 0 0 0 0 0 0 0 97 97 41 41 True False True +scpipe scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing To update http://bioconductor.org/packages/release/bioc/html/scPipe.html Transcriptomics, Single Cell scpipe 2018-08-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 284 632 34 38 786 786 61 61 1 1 1 1 1071 1419 96 100 True False True +scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred 2020-04-07 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred 1.0.2 scpred-cli 0.1.0 0 0 4 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 5 5 0 0 0 0 0 0 0 0 25 25 5 5 True False True +seurat seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 To update https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat 2018-07-09 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 4.0.0 seurat-scripts 4.4.0 14 14 14 11 14 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 0 0 0 0 0 2296 2328 673 676 141 141 39 39 0 0 0 0 2437 2469 712 715 True False True +seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics To update https://satijalab.org/seurat/ Single Cell, Transcriptomics, Sequence Analysis seurat 2020-07-22 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 5.0 r-seurat 3.0.2 1 1 7 1 1 1 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 121 121 11 11 32 32 5 5 0 0 0 0 153 153 16 16 True False True +sinto sinto_barcode, sinto_fragments Sinto single-cell analysis tools Up-to-date https://github.com/timoast/sinto Single Cell, Epigenetics 2023-04-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto 0.10.1 sinto 0.10.1 2 2 2 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 284 284 70 70 165 165 38 38 14 14 2 2 463 463 110 110 True False True +slamdunk alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads Up-to-date http://t-neumann.github.io/slamdunk RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers slamdunk 2019-01-20 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk 0.4.3 slamdunk 0.4.3 2 0 2 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 346 362 16 16 872 872 67 67 0 0 0 0 1218 1234 83 83 True False False +sleuth sleuth Sleuth is a program for differential analysis of RNA-Seq data. sleuth sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-seq, Gene expression, Statistics and probability Up-to-date https://github.com/pachterlab/sleuth Transcriptomics, RNA, Statistics sleuth 2023-05-31 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth 0.30.1 r-sleuth 0.30.1 Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 141 141 26 26 0 0 0 0 0 0 0 0 141 141 26 26 True False False +snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis To update https://kzhang.org/SnapATAC2/ Single Cell, Epigenetics snapatac2 2024-05-16 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 2.6.4 4 4 4 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1817 1817 14 14 4 4 2 2 136 136 4 4 1957 1957 20 20 True False True +spapros spapros_evaluation, spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. Up-to-date https://github.com/theislab/spapros Single Cell, Transcriptomics, Sequence Analysis spapros 2024-08-25 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros 0.1.5 spapros 0.1.5 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 True False True +star_fusion star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR To update https://github.com/STAR-Fusion/STAR-Fusion Sequence Analysis, Transcriptomics star_fusion 2015-10-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion 0.5.4-3+galaxy1 star-fusion 1.13.0 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1312 1383 82 95 2198 3076 234 303 173 173 3 3 3683 4632 319 401 True False False +stringtie stringtie, stringtie_merge StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. stringtie stringtie StringTie 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. Transcriptome assembly, RNA-Seq analysis Transcriptomics, RNA-seq Up-to-date http://ccb.jhu.edu/software/stringtie/ Transcriptomics stringtie 2019-09-05 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie 2.2.3 stringtie 2.2.3 Transcriptome assembly, RNA-Seq analysis Transcriptomics 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 178677 187728 4972 5347 320780 407379 10825 15171 26375 28921 1032 1167 525832 624028 16829 21685 True False False +tophat_fusion_post tophat_fusion_post Wrapper for Tophat-Fusion post step To update Transcriptomics tophat_fusion_post 2014-01-27 devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post 0.1 blast+ 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 220 242 41 46 6 814 2 191 100 120 8 12 326 1176 51 249 True False False +transdecoder transdecoder TransDecoder finds coding regions within transcripts TransDecoder TransDecoder TransDecoder 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. Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing To update https://transdecoder.github.io/ Transcriptomics, RNA transdecoder 2015-11-09 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder 5.5.0 transdecoder 5.7.1 Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5964 6418 944 970 5450 5450 1066 1066 2610 2796 317 344 14024 14664 2327 2380 True False False +trinity trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity trinity Trinity 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. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts To update https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA 2019-11-13 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity 2.15.1 trinity 2.15.2 Transcriptome assembly Transcriptomics, Gene transcripts 9 13 13 13 9 13 13 13 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 0 0 11 0 0 1 0 0 0 11 13 12 0 35698 39132 4376 4632 44509 44509 6714 6714 21883 23889 1924 2070 102090 107530 13014 13416 True False False +trinotate trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. trinotate trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Gene functional annotation Gene expression, Transcriptomics To update https://trinotate.github.io/ Transcriptomics, RNA trinotate 2016-11-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate 3.2.2 trinotate 4.0.2 Gene functional annotation Transcriptomics 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1968 2080 374 390 1825 1825 527 527 862 1060 161 195 4655 4965 1062 1112 True False False +tximport tximport Wrapper for the Bioconductor package tximport tximport tximport tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows Up-to-date http://bioconductor.org/packages/tximport/ Transcriptomics tximport 2019-11-27 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport 1.30.0 bioconductor-tximport 1.30.0 Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1802 1802 225 225 6963 6963 904 904 0 0 0 0 8765 8765 1129 1129 True False False +ucsc-cell-browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser 2018-09-11 ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser 1.0.0+galaxy1 ucsc-cell-browser 1.2.8 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 965 975 178 181 0 0 0 0 0 0 0 0 965 975 178 181 True False True +umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Up-to-date https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics, Single Cell 2021-07-15 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.5 umi_tools 1.1.5 Sequencing quality control Sequence sites, features and motifs, Quality affairs 5 5 5 5 5 5 5 5 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 5 0 0 0 0 0 0 3 5 5 0 55050 68123 1090 1223 9001 9001 906 906 12444 12444 187 187 76495 89568 2183 2316 True False True +velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. Up-to-date http://velocyto.org/ Transcriptomics, Single Cell velocyto 2021-04-30 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto 0.17.17 velocyto.py 0.17.17 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 4 4 22 22 6 6 16 16 1 1 45 45 11 11 True False True +volcanoplot volcanoplot Tool to create a Volcano Plot To update https://ggplot2.tidyverse.org/ Visualization, Transcriptomics, Statistics volcanoplot 2018-10-14 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 0.0.6 r-ggplot2 2.2.1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 34917 36852 3670 3786 54931 54931 5597 5597 7183 7183 905 905 97031 98966 10172 10288 True False True diff --git a/communities/spoc/resources/tools_wordcloud.png b/communities/spoc/resources/tools_wordcloud.png index 25c0e98a..4947046d 100644 Binary files a/communities/spoc/resources/tools_wordcloud.png and b/communities/spoc/resources/tools_wordcloud.png differ