Repositories list

• single-cell

  Public

  gustaveroussy/single-cell’s past year of commit activity
  R

  •

  GNU General Public License v3.0

  •44 forks•77 stars•00 issues•00 pull requests•Updated Apr 14, 2026Apr 14, 2026

• alberge-lab-website

  Public
  Source code for Alberge Lab

  HTML

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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 9, 2026Apr 9, 2026

• training_bigr

  Public

  gustaveroussy/training_bigr’s past year of commit activity
  This repository containing all trainings from bioinformatics platform of Gustave Roussy

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 17, 2026Mar 17, 2026

• LaurieMengerLab

  Public
  HTML

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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 24, 2026Feb 24, 2026

• FG-Lab

  Public
  R

  •77 forks•1414 stars•33 issues•00 pull requests•Updated Feb 12, 2026Feb 12, 2026

• IFSBM-bigdata

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

  R

  •33 forks•11 star•00 issues•00 pull requests•Updated Dec 19, 2025Dec 19, 2025

• ICARUS-01_Public

  Public

  gustaveroussy/ICARUS-01_Public’s past year of commit activity
  Public code supporting analyses presented in ICARUS 01 breast and lung papers.

  Python

  •

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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 26, 2025Sep 26, 2025

• EaCoN

  Public
  Easy Copy Number !

  rmicroarraysegmentation+ 2

  rmicroarraysegmentationcopy-numberexome-sequencing

  R

  •

  MIT License

  •1515 forks•2121 stars•77 issues•11 pull request•Updated Aug 27, 2025Aug 27, 2025

• prismtoolbox

  Public
  Toolbox for histopathology image analysis

  toolboxembeddingspreprocessing+ 2

  toolboxembeddingspreprocessinghistopathologynuclei-segmentation

  Python

  •

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

  •00 forks•77 stars•00 issues•00 pull requests•Updated Aug 18, 2025Aug 18, 2025

• EaCoNiC

  Public

  gustaveroussy/EaCoNiC’s past year of commit activity
  Easy Copy Number, in Cohort !

  R

  •

  MIT License

  •00 forks•00 stars•11 issue•00 pull requests•Updated Jul 12, 2025Jul 12, 2025

• bigr_rna_editing

  Public

  gustaveroussy/bigr_rna_editing’s past year of commit activity
  This pipeline uses SPRINT and RNAEditingIndexer to identify editing event from RNA-seq

  Python

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 10, 2025Mar 10, 2025

• PipelineAgentService

  Public

  gustaveroussy/PipelineAgentService’s past year of commit activity
  PipelineAgentService is a large language model (LLM)-based application designed for the automated management of data processing tasks.

  pipelineworkflow-automationrq+ 13

  pipelineworkflow-automationrqhuman-in-the-loopreason-reactragfastapigoogle-cloud-apiai-agentchain-of-thought+ 6

  Python

  •

  MIT License

  •22 forks•33 stars•00 issues•00 pull requests•Updated Mar 5, 2025Mar 5, 2025

• Rstuff

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

  R

  •

  GNU General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Dec 3, 2024Dec 3, 2024

• CFS

  Public

  gustaveroussy/CFS’s past year of commit activity
  R package using ICA based method for spatial transcriptomics analysis (Visium/Slide-seq/CosMX/MERSCOPE)

  rspatialspatial-data+ 4

  rspatialspatial-datainteractionicaspatial-transcriptomicsvisium

  R

  •33 forks•99 stars•33 issues•00 pull requests•Updated Oct 23, 2024Oct 23, 2024

• apt.cytoscan.2.11.7

  Public
  apt-copynumber-cyto-ssa v2.11.7

  R

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•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+ 1

  rmicroarraynormalizationaffymetrix

  R

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 8, 2024Jul 8, 2024

• DAISY_Public

  Public

  gustaveroussy/DAISY_Public’s past year of commit activity
  Public repository supporting the paper of the DAISY study.

  Python

  •22 forks•00 stars•00 issues•00 pull requests•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

  •11 fork•99 stars•00 issues•00 pull requests•Updated Feb 5, 2024Feb 5, 2024

• OSIRIS-RWD

  Public
  Implementation guide - SOs

  22 forks•00 stars•00 issues•00 pull requests•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

  •00 forks•22 stars•00 issues•00 pull requests•Updated Sep 29, 2023Sep 29, 2023

• single-cell-DNA

  Public
  Single-cell DNA-seq Tapestri pipeline

  Python

  •11 fork•00 stars•11 issue•00 pull requests•Updated Sep 26, 2023Sep 26, 2023

• MAPPYACTs_PDX

  Public

  gustaveroussy/MAPPYACTs_PDX’s past year of commit activity
  R notebooks used to produce a part of the figures for the analysis of MAPPYACTS PDX and associated patient samples

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Aug 22, 2023Aug 22, 2023

• PDXBiobankAnalysis

  Public
  Scripts to analyse expression of PDX from MAPYYACTS cohort

  MATLAB

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 26, 2023Jul 26, 2023

• MAPPYACTS

  Public
  Codes to Figure in "A biobank of pediatric patient-derived-xenograft models in cancer precision medicine trial MAPPYACTS for relapsed and refractory tumors"

  R

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 26, 2023Jul 26, 2023

• CustOmics

  Public
  A deep-learning framework for multi-omics integration

  Jupyter Notebook

  •

  MIT License

  •1010 forks•00 stars•00 issues•00 pull requests•Updated Jul 6, 2023Jul 6, 2023

• TCGA_Facets

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

  Python

  •11 fork•00 stars•00 issues•00 pull requests•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

  •33 forks•00 stars•00 issues•00 pull requests•Updated Dec 13, 2022Dec 13, 2022

• snakemake-wrappers

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

  CAP CDS

  •210210 forks•00 stars•00 issues•00 pull requests•Updated Dec 12, 2022Dec 12, 2022

• SingleCellTK

  Public

  gustaveroussy/SingleCellTK’s past year of commit activity
  SingleCellTK with severside RDS IO

  HTML

  •

  Other

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 15, 2022Nov 15, 2022

• DeViSE

  Public
  Detection and visualization of splicing events

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 31, 2022Oct 31, 2022