Pinned Repositories
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
fair_bowtie2_mapping
Align reads over a reference genome, filter aligned-reads, and mark duplicates
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_genome_indexer
Download and index Ensembl sequences and annotations
fair_macs2_calling
Snakemake workflow used to call peaks with Macs2
fair_rnaseq_salmon_quant
Snakemake workflow designed to perform RNASeq transcrpotime expression estimation with Salmon
snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
tdayris's Repositories
tdayris/cel-cnv-eacon
Perform Cytoscans/Oncoscans CNV analysis with EaCoN
tdayris/snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
tdayris/bigr_epicure_pipeline
Snakemake pipeline for Epicure analyses
tdayris/bigr_templates
Several templates for Open-on-demand and procedures
tdayris/Cpp-Translate
A c++ project for translating c++ in many languages (including std) (it is a joke)
tdayris/EaCoN
Easy Copy Number !
tdayris/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"
tdayris/environments
A cookiecutter for sharable Conda-environments among IGR infrastructure
tdayris/fair_bowtie2_mapping
Align reads over a reference genome, filter aligned-reads, and mark duplicates
tdayris/fair_fastqc_multiqc
Perform basic QC over sequenced data
tdayris/fair_gatk_mutect2
Snakemake workflow used to call germline and/or somatic variants with GATK Mutect2
tdayris/fair_genome_indexer
Download and index Ensembl sequences and annotations
tdayris/fair_macs2_calling
Snakemake workflow used to call peaks with Macs2
tdayris/fair_rnaseq_salmon_quant
Snakemake workflow designed to perform RNASeq transcrpotime expression estimation with Salmon
tdayris/esperanto
tdayris/fair_bismark_pipeline
Snakemake workflow used to analyse bisulfite treated sequencing with Bismark
tdayris/fair_cnv_facets
Snakemake workflow designed to call CNV using Facets
tdayris/fair_gatk_mutect_somatic
Snakemake workflow used to call somatic variants with GATK Mutect2
tdayris/fair_rnaseq_deseq2
Snakemake workflow used to call differentially expressed genes with DESeq2 on bulk RNA-Seq.
tdayris/FAIR_smk
tdayris/fair_star_mapping
Sanekamke workflow used to align reads with STAR
tdayris/irods_copy
Snakemake workflow used to download iRODS data and prepare sample description on Gustave Roussy's Flamingo cluster
tdayris/miniconda-strict
a miniconda docker/singularity image with strict channels priorities by default
tdayris/rna-dge-salmon-deseq2
Perform differential analysis from FastQ files with Salmon, tximport, and DESeq2
tdayris/scTKcomp
A supplementary for singleCellTK, filling some "holes" (empty droplets filtering, cell cycle scoring)
tdayris/single-cell
tdayris/singleCellTK
Interactively analyze single cell genomic data
tdayris/snakemake
This is the development home of the workflow management system Snakemake. For general information, see
tdayris/snakemake-executor-plugin-slurm-gustave-roussy
Snakemake plugin executor with special values for GUstave Roussy's Flamingo
tdayris/snakemake-wrapper-utils
Utility functions and classes shared between Snakemake wrappers