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 that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)
SuGR
Gustave Roussy's Repositories
gustaveroussy/rna-count-kallisto
Estimate fastq-formatted read abundace in RNA-Seq analysis with Kallisto
gustaveroussy/pileup2vcf
Simple variant caller - Please update to the latest version !
gustaveroussy/advancedQC
gustaveroussy/apt.oncoscan.2.4.0
Affymetrix OncoScan / OncoScan_CNV processing using apt-copynumber-onco-ssa (2.4.0)
gustaveroussy/Rstuff
A compilation of R scripts for different, widely diverse purposes
gustaveroussy/SuGR
gustaveroussy/vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
gustaveroussy/wes-snp-bwa-mutect2-annovar
Reference pipeline for somatic SNP detection using BWA for mapping, Mutect2 for calling and Annovar for annotation
gustaveroussy/Presentations
gustaveroussy/98drivers
analysis pipeline for cancer whole genome
gustaveroussy/apt.snp6.1.20.0
Affymetrix GenomeWideSNP_6 processing using apt-copynumber-workflow (1.20.0)
gustaveroussy/cBioPortal
cBioPortal related stuff
gustaveroussy/Cours
Supports de cours Gustave Roussy
gustaveroussy/icgc-tools
Convert icgc data to common bioinformatics format
gustaveroussy/mBC_WES_Fabrice_Andre_2019
gustaveroussy/OSIRIS
gustaveroussy/rna-count-salmon
Count your fastq-formatted rna-seq reads with Salmon
gustaveroussy/rnafusion
RNA-seq analysis pipeline for detection gene-fusions
gustaveroussy/Stage_M2_Marie
gustaveroussy/tool-mutect2-tumornormal
Snakemake wrapper for GATK mutect, tumor/normal mode
gustaveroussy/tool-samtools-fixmate
Snakemake wrapper for samtools fixmate
gustaveroussy/tool-samtools-markdup
Snakemake wrapper for samtools markdup
gustaveroussy/vcf-annotate-snpeff-snpsift
Snakemake workflow designed to annotate VCF files withe SnpEff / SniSift