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bigr_epicure_pipeline

Snakemake pipeline for Epicure analyses

bigr_templates

Several templates for Open-on-demand and procedures

cel-cnv-eacon

Perform Cytoscans/Oncoscans CNV analysis with EaCoN

cpp-translate

A c++ project for translating c++ in many languages (including std) (it is a joke)

eacon

Easy Copy Number !

ebaii

Supports de cours de l'Ecole de Bioinformatique Aviesan - IFB - Inserm "Initiation au traitement des données de génomique obtenues par séquençage à haut débit"

environments

A cookiecutter for sharable Conda-environments among IGR infrastructure

esperanto

fair_bismark_pipeline

Snakemake workflow used to analyse bisulfite treated sequencing with Bismark

fair_bowtie2_mapping

Align reads over a reference genome, filter aligned-reads, and mark duplicates

fair_cnv_facets

Snakemake workflow designed to call CNV using Facets

fair_fastqc_multiqc

Perform basic QC over sequenced data

fair_gatk_mutect2

Snakemake workflow used to call germline and/or somatic variants with GATK Mutect2

fair_gatk_mutect_somatic

Snakemake workflow used to call somatic variants with GATK Mutect2

fair_genome_indexer

Download and index Ensembl sequences and annotations

fair_macs2_calling

Snakemake workflow used to call peaks with Macs2

fair_rnaseq_deseq2

Snakemake workflow used to call differentially expressed genes with DESeq2 on bulk RNA-Seq.

fair_rnaseq_salmon_quant

Snakemake workflow designed to perform RNASeq transcrpotime expression estimation with Salmon

fair_smk

fair_star_mapping

Sanekamke workflow used to align reads with STAR

irods_copy

Snakemake workflow used to download iRODS data and prepare sample description on Gustave Roussy's Flamingo cluster

miniconda-strict

a miniconda docker/singularity image with strict channels priorities by default

projects

These are my snakefiles for each projects

rna-dge-salmon-deseq2

Perform differential analysis from FastQ files with Salmon, tximport, and DESeq2

sctkcomp

A supplementary for singleCellTK, filling some "holes" (empty droplets filtering, cell cycle scoring)

single-cell

singlecelltk

Interactively analyze single cell genomic data

snakemake

This is the development home of the workflow management system Snakemake. For general information, see

snakemake-executor-plugin-slurm-gustave-roussy

Snakemake plugin executor with special values for GUstave Roussy's Flamingo

snakemake-wrapper-utils

Utility functions and classes shared between Snakemake wrappers