Pinned Repositories
CFS
R package using ICA based method for spatial transcriptomics analysis (Visium/Slide-seq/CosMX/MERSCOPE)
EaCoN
Easy Copy Number !
FG-Lab
MetaPRISM_Public
Code support all the analyses and figures for the MetaPRISM paper.
pileup2vcf
Simple variant caller - Please update to the latest version !
prismtoolbox
Toolbox for histopathology image analysis
rna-count-kallisto
Estimate fastq-formatted read abundace in RNA-Seq analysis with Kallisto
single-cell
sopa
Technology-invariant pipeline for spatial omics analysis (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / ...) that scales to millions of cells
SuGR
Gustave Roussy's Repositories
gustaveroussy/sopa
Technology-invariant pipeline for spatial omics analysis (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / ...) that scales to millions of cells
gustaveroussy/EaCoN
Easy Copy Number !
gustaveroussy/FG-Lab
gustaveroussy/CFS
R package using ICA based method for spatial transcriptomics analysis (Visium/Slide-seq/CosMX/MERSCOPE)
gustaveroussy/MetaPRISM_Public
Code support all the analyses and figures for the MetaPRISM paper.
gustaveroussy/single-cell
gustaveroussy/prismtoolbox
Toolbox for histopathology image analysis
gustaveroussy/apt.cytoscan.2.4.0
Affymetrix CytoScan (750k / HD) processing using apt-copynumber-cyto-ssa (2.4.0)
gustaveroussy/IFSBM-bigdata
Repository with the contents for the coding exercices and the lectures of module 11 of ISFBM university diploma.
gustaveroussy/bigr_long-reads_bulk
Long-reads Bulk DNA-seq pipeline
gustaveroussy/single-cell-DNA
Single-cell DNA-seq Tapestri pipeline
gustaveroussy/apt.cytoscan.2.11.7
apt-copynumber-cyto-ssa v2.11.7
gustaveroussy/bigr_rna_editing
This pipeline uses SPRINT and RNAEditingIndexer to identify editing event from RNA-seq
gustaveroussy/CTAP
gustaveroussy/CustOmics
A deep-learning framework for multi-omics integration
gustaveroussy/DAISY_Public
Public repository supporting the paper of the DAISY study.
gustaveroussy/docker-registry
gustaveroussy/EaCoN.cache
A dataset package that contains cached information for genome, chromosomes and genomic annotations, to be used with EaCoN / EaCoNiC.
gustaveroussy/EaCoNiC
Easy Copy Number, in Cohort !
gustaveroussy/macroverse
gustaveroussy/MultiQC_SAV
MultiQC plugin replicating the most used plots and tables from Illumina's SAV
gustaveroussy/OSIRIS-RWD
Implementation guide - SOs
gustaveroussy/OSTEOMICS_pub
Code associated to the publication : "Immune infiltrate and tumor microenvironment transcriptional programs stratify pediatric osteosarcoma into prognostic groups at diagnosis"
gustaveroussy/PipelineJar
gustaveroussy/pipline_identitovigilence_3Allele
pipline qui permet de reperer les problèmes des echantillions
gustaveroussy/SingleCellTK
SingleCellTK with severside RDS IO
gustaveroussy/snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
gustaveroussy/TCGA_Facets
Snakemake pipeline for running FACETS on all WXS TCGA samples.
gustaveroussy/training_bigr
This repository containing all trainings from bioinformatics platform of Gustave Roussy
gustaveroussy/twist-target-methylation-sequencing
Analyzing Twist Targeted Methylation Sequencing Data Using the Twist Human Methylome Panel