Repositories list

• sopa

  Public
  Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)

  snakemakepipelinememory-management+ 5generalizationspatial-transcriptomicsspatialdatamultiplexed-imagingspatial-omics

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •16•143•29•1•Updated Nov 25, 2024Nov 25, 2024

• training_bigr

  Public
  This repository containing all trainings from bioinformatics platform of Gustave Roussy

  HTML

  •0•0•0•0•Updated Oct 27, 2024Oct 27, 2024

• CFS

  Public
  R package using ICA based method for spatial transcriptomics analysis (Visium/Slide-seq/CosMX/MERSCOPE)

  rspatialspatial-data+ 4interactionicaspatial-transcriptomicsvisium

  R

  •2•7•3•0•Updated Oct 23, 2024Oct 23, 2024

• FG-Lab

  Public
  R

  •5•8•3•0•Updated Sep 9, 2024Sep 9, 2024

• prismtoolbox

  Public
  Toolbox for histopathology image analysis

  toolboxembeddingspreprocessing+ 2histopathologynuclei-segmentation

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•4•0•0•Updated Aug 22, 2024Aug 22, 2024

• apt.cytoscan.2.11.7

  Public
  apt-copynumber-cyto-ssa v2.11.7

  R

  •

  MIT License

  •0•0•0•0•Updated Jul 8, 2024Jul 8, 2024

• apt.cytoscan.2.4.0

  Public
  Affymetrix CytoScan (750k / HD) processing using apt-copynumber-cyto-ssa (2.4.0)

  rmicroarraynormalization+ 1affymetrix

  R

  •0•1•0•0•Updated Jul 8, 2024Jul 8, 2024

• bigr_rna_editing

  Public
  This pipeline uses SPRINT and RNAEditingIndexer to identify editing event from RNA-seq

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jun 21, 2024Jun 21, 2024

• single-cell

  Public
  R

  •

  GNU General Public License v3.0

  •4•5•0•1•Updated Jun 7, 2024Jun 7, 2024

• DAISY_Public

  Public
  Public repository supporting the paper of the DAISY study.

  Python

  •2•0•0•0•Updated Apr 8, 2024Apr 8, 2024

• MetaPRISM_Public

  Public
  Code support all the analyses and figures for the MetaPRISM paper.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•6•0•0•Updated Feb 5, 2024Feb 5, 2024

• IFSBM-bigdata

  Public
  Repository with the contents for the coding exercices and the lectures of module 11 of ISFBM university diploma.

  HTML

  •3•0•0•0•Updated Feb 2, 2024Feb 2, 2024

• OSIRIS-RWD

  Public
  Implementation guide - SOs

  2•0•0•0•Updated Oct 20, 2023Oct 20, 2023

• twist-target-methylation-sequencing

  Public
  Analyzing Twist Targeted Methylation Sequencing Data Using the Twist Human Methylome Panel

  Python

  •

  MIT License

  •0•0•0•0•Updated Sep 29, 2023Sep 29, 2023

• single-cell-DNA

  Public
  Single-cell DNA-seq Tapestri pipeline

  Python

  •1•0•1•0•Updated Sep 26, 2023Sep 26, 2023

• CustOmics

  Public
  A deep-learning framework for multi-omics integration

  Jupyter Notebook

  •

  MIT License

  •7•0•0•0•Updated Jul 6, 2023Jul 6, 2023

• TCGA_Facets

  Public
  Snakemake pipeline for running FACETS on all WXS TCGA samples.

  Python

  •1•0•0•0•Updated Mar 2, 2023Mar 2, 2023

• MultiQC_SAV

  Public
  MultiQC plugin replicating the most used plots and tables from Illumina's SAV

  Python

  •

  MIT License

  •1•0•0•0•Updated Dec 13, 2022Dec 13, 2022

• snakemake-wrappers

  Public
  This is the development home of the Snakemake wrapper repository, see

  CAP CDS

  •186•0•0•0•Updated Dec 12, 2022Dec 12, 2022

• SingleCellTK

  Public
  SingleCellTK with severside RDS IO

  HTML

  •

  Other

  •0•0•0•0•Updated Nov 15, 2022Nov 15, 2022

• docker-registry

  Public
  Dockerfile

  •0•0•0•0•Updated Jul 27, 2022Jul 27, 2022

• EaCoNiC

  Public
  Easy Copy Number, in Cohort !

  R

  •

  MIT License

  •0•0•1•0•Updated Jun 30, 2022Jun 30, 2022

• OSTEOMICS_pub

  Public
  Code associated to the publication : "Immune infiltrate and tumor microenvironment transcriptional programs stratify pediatric osteosarcoma into prognostic groups at diagnosis"

  R

  •0•0•0•0•Updated Dec 28, 2021Dec 28, 2021

• EaCoN

  Public
  Easy Copy Number !

  rmicroarraysegmentation+ 2copy-numberexome-sequencing

  R

  •

  MIT License

  •14•21•7•0•Updated Oct 18, 2021Oct 18, 2021

• pipline_identitovigilence_3Allele

  Public
  pipline qui permet de reperer les problèmes des echantillions

  Java

  •0•0•0•0•Updated Sep 24, 2021Sep 24, 2021

• PipelineJar

  Public
  0•0•0•0•Updated Jul 9, 2021Jul 9, 2021

• EaCoN.cache

  Public
  A dataset package that contains cached information for genome, chromosomes and genomic annotations, to be used with EaCoN / EaCoNiC.

  MIT License

  •0•0•0•0•Updated Jul 1, 2021Jul 1, 2021

• macroverse

  Public
  MIT License

  •0•0•0•0•Updated Mar 29, 2021Mar 29, 2021

• CTAP

  Public
  Python

  •1•0•0•0•Updated Mar 25, 2021Mar 25, 2021

• Rstuff

  Public
  A compilation of R scripts for different, widely diverse purposes

  R

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Oct 16, 2020Oct 16, 2020