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snakemake-wrappers Public
Forked from snakemake/snakemake-wrappersThis is the development home of the Snakemake wrapper repository, see
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snakemake-wrapper-utils Public
Forked from snakemake/snakemake-wrapper-utilsUtility functions and classes shared between Snakemake wrappers
Python MIT License UpdatedMar 24, 2026 -
Snakemake plugin executor with special values for GUstave Roussy's Flamingo
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fair_recount_pump Public
Run Recount-pump with snakemake workflow interface and conda deployment
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fair_genome_indexer Public
Download and index Ensembl sequences and annotations, remove non-canonical chromosimes, remove low TSL, index with multiple tools
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fair_fastqc_multiqc Public
Perform basic QC over sequenced data
Python MIT License UpdatedJun 18, 2025 -
fair_bowtie2_mapping Public
Align reads over a reference genome, filter aligned-reads, and mark duplicates
Python MIT License UpdatedMar 20, 2025 -
fair_gatk_mutect2 Public
Snakemake workflow used to call germline and/or somatic variants with GATK Mutect2
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fair_star_mapping Public
Sanekamke workflow used to align reads with STAR
Python MIT License UpdatedMar 10, 2025 -
fair_macs2_calling Public
Snakemake workflow used to call peaks with Macs2
Python MIT License UpdatedMar 7, 2025 -
MultiQC Public
Forked from MultiQC/MultiQCAggregate results from bioinformatics analyses across many samples into a single report.
JavaScript GNU General Public License v3.0 UpdatedFeb 5, 2025 -
fair_rnaseq_salmon_quant Public
Snakemake workflow designed to perform RNASeq transcrpotime expression estimation with Salmon
Python MIT License UpdatedFeb 5, 2025 -
fair_cnv_facets Public
Snakemake workflow designed to call CNV using Facets
Python MIT License UpdatedDec 9, 2024 -
snakemake Public
Forked from snakemake/snakemakeThis is the development home of the workflow management system Snakemake. For general information, see
HTML MIT License UpdatedOct 11, 2024 -
single-cell Public
Forked from gustaveroussy/single-cellR GNU General Public License v3.0 UpdatedJun 7, 2024 -
Cpp-Translate Public
Forked from Supercip971/Cpp-TranslateA c++ project for translating c++ in many languages (including std) (it is a joke)
C++ MIT License UpdatedApr 18, 2024 -
fair_rnaseq_deseq2 Public
Snakemake workflow used to call differentially expressed genes with DESeq2 on bulk RNA-Seq.
Python MIT License UpdatedFeb 29, 2024 -
bigr_epicure_pipeline Public
Snakemake pipeline for Epicure analyses
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fair_gatk_mutect_somatic Public
Snakemake workflow used to call somatic variants with GATK Mutect2
Python MIT License UpdatedFeb 19, 2024 -
fair_bismark_pipeline Public
Snakemake workflow used to analyse bisulfite treated sequencing with Bismark
Python MIT License UpdatedNov 23, 2023 -
EBAII Public
Forked from IFB-ElixirFr/EBAIISupports de cours de l'Ecole de Bioinformatique Aviesan - IFB - Inserm "Initiation au traitement des données de génomique obtenues par séquençage à haut débit"
HTML GNU General Public License v3.0 UpdatedOct 25, 2023 -
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singleCellTK Public
Forked from compbiomed/singleCellTKInteractively analyze single cell genomic data
R Other UpdatedNov 10, 2022 -
scTKcomp Public
Forked from aoumess/scTKcompA supplementary for singleCellTK, filling some "holes" (empty droplets filtering, cell cycle scoring)
R MIT License UpdatedOct 25, 2022 -
rna-dge-salmon-deseq2 Public archive
Forked from tdayris-perso/rna-dge-salmon-deseq2Perform differential analysis from FastQ files with Salmon, tximport, and DESeq2
Python GNU General Public License v3.0 UpdatedAug 17, 2021 -
cel-cnv-eacon Public archive
Perform Cytoscans/Oncoscans CNV analysis with EaCoN
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yawn Public
A bunch of scripts for actions I have to do on a regular basis
Python GNU General Public License v3.0 UpdatedMar 11, 2020
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