gustaveroussy Goto Github PK

98drivers

analysis pipeline for cancer whole genome

advancedqc

apt.cytoscan.2.11.7

apt-copynumber-cyto-ssa v2.11.7

apt.cytoscan.2.4.0

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

apt.oncoscan.2.4.0

Affymetrix OncoScan / OncoScan_CNV processing using apt-copynumber-onco-ssa (2.4.0)

apt.snp6.1.20.0

Affymetrix GenomeWideSNP_6 processing using apt-copynumber-workflow (1.20.0)

bigr_long-reads_bulk

Long-reads Bulk DNA-seq pipeline

bigr_rna_editing

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

cbioportal

cBioPortal related stuff

cfs

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

cours

Supports de cours Gustave Roussy

ctap

customics

A deep-learning framework for multi-omics integration

daisy_public

Public repository supporting the paper of the DAISY study.

docker-registry

eacon

Easy Copy Number !

eacon.cache

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

eaconic

Easy Copy Number, in Cohort !

fg-lab

icgc-tools

Convert icgc data to common bioinformatics format

ifsbm-bigdata

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

macroverse

mbc_wes_fabrice_andre_2019

metaprism_public

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

multiqc_sav

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

osiris

osiris-rwd

Implementation guide - SOs

osteomics_pub

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

pileup2vcf

Simple variant caller - Please update to the latest version !

pipelinejar