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)

  pipelinesegmentationspatial-transcriptomics+ 3spatialdatamultiplexed-imagingspatial-omics

  Python

  •

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

  •36•214•31•3•Updated Aug 20, 2025Aug 20, 2025

• training_bigr

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

  HTML

  •0•0•0•0•Updated Aug 19, 2025Aug 19, 2025

• prismtoolbox

  Public
  Toolbox for histopathology image analysis

  toolboxembeddingspreprocessing+ 2histopathologynuclei-segmentation

  Python

  •

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

  •0•6•0•0•Updated Aug 18, 2025Aug 18, 2025

• ICARUS-01_Public

  Public
  Public code supporting analyses presented in ICARUS 01 breast and lung papers.

  Python

  •

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

  •0•0•0•0•Updated Aug 18, 2025Aug 18, 2025

• EaCoNiC

  Public
  Easy Copy Number, in Cohort !

  R

  •

  MIT License

  •0•0•1•0•Updated Jul 12, 2025Jul 12, 2025

• EaCoN

  Public
  Easy Copy Number !

  rmicroarraysegmentation+ 2copy-numberexome-sequencing

  R

  •

  MIT License

  •14•21•7•0•Updated Jul 11, 2025Jul 11, 2025

• single-cell

  Public
  R

  •

  GNU General Public License v3.0

  •4•6•0•1•Updated Mar 16, 2025Mar 16, 2025

• 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 Mar 10, 2025Mar 10, 2025

• PipelineAgentService

  Public
  PipelineAgentService is a large language model (LLM)-based application designed for the automated management of data processing tasks.

  pipelineworkflow-automationrq+ 13human-in-the-loopreason-reactragfastapigoogle-cloud-apiai-agentchain-of-thought+ 6

  Python

  •

  MIT License

  •2•3•0•0•Updated Mar 5, 2025Mar 5, 2025

• LaurieMengerLab

  Public
  HTML

  •

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

  •0•0•0•0•Updated Feb 3, 2025Feb 3, 2025

• FG-Lab

  Public
  R

  •5•10•3•0•Updated Jan 29, 2025Jan 29, 2025

• IFSBM-bigdata

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

  R

  •3•1•0•0•Updated Jan 6, 2025Jan 6, 2025

• Rstuff

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

  R

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Dec 3, 2024Dec 3, 2024

• CFS

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

  rspatialspatial-data+ 4interactionicaspatial-transcriptomicsvisium

  R

  •3•8•3•0•Updated Oct 23, 2024Oct 23, 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

• 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•8•0•0•Updated Feb 5, 2024Feb 5, 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

• MAPPYACTs_PDX

  Public
  R notebooks used to produce a part of the figures for the analysis of MAPPYACTS PDX and associated patient samples

  MIT License

  •1•0•0•0•Updated Aug 22, 2023Aug 22, 2023

• PDXBiobankAnalysis

  Public
  Scripts to analyse expression of PDX from MAPYYACTS cohort

  MATLAB

  •

  MIT License

  •1•0•0•0•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

  •1•0•0•0•Updated Jul 26, 2023Jul 26, 2023

• CustOmics

  Public
  A deep-learning framework for multi-omics integration

  Jupyter Notebook

  •

  MIT License

  •8•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

  •195•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

• DeViSE

  Public
  Detection and visualization of splicing events

  HTML

  •0•0•0•0•Updated Oct 31, 2022Oct 31, 2022