tdayris

This is the development home of the Snakemake wrapper repository, see

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

Run Recount-pump with snakemake workflow interface and conda deployment

Download and index Ensembl sequences and annotations, remove non-canonical chromosimes, remove low TSL, index with multiple tools

No description provided.

Perform basic QC over sequenced data

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

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

Sanekamke workflow used to align reads with STAR

Snakemake workflow used to call peaks with Macs2

Aggregate results from bioinformatics analyses across many samples into a single report.

Snakemake workflow designed to perform RNASeq transcrpotime expression estimation with Salmon

Snakemake workflow designed to call CNV using Facets

Utility functions and classes shared between Snakemake wrappers

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

No description provided.

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

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

Snakemake workflow used to call somatic variants with GATK Mutect2

Snakemake workflow used to analyse bisulfite treated sequencing with Bismark

No description provided.

Snakemake pipeline for Epicure analyses

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

Perform Cytoscans/Oncoscans CNV analysis with EaCoN

Interactively analyze single cell genomic data

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

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

Easy Copy Number !

A bunch of scripts for actions I have to do on a regular basis