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alignment4lanes-nf

Whole Exome/Whole Genome Sequencing alignment pipeline

bash-tips-tricks

Tips and tricks (mainly for comp. gen.) in the Bash language

cancergenomicscloud_tutorial

Tutorial for the sevenbridges cancer genomics cloud

curriculum

Repository for my latex CV based on awesome-CV from @posquit0

fastqc-nf

Nextflow pipeline for fastqc

hyperstack

Nextflow pipeline to run the intercept method on needlestack calling with a step of FDR computation with ML

lesson-notes

Repository containing notes from lessons in field of statistics, bioinformatics or even molecular biology

liftover-nf

Convert BED/VCF files between two genomes with nextflow

nf-scripts

folder of small nextflow scripts

nmf_vcf-nf

nextflow pipeline extracting mutational signatures from VCF files

notes

Folder with notes about how to use new tools

pyclone_clonevol_analysis

Intra-tumor heterogeneity analysis with pyclone and clonevol

r-tips-tricks

Piece of R code

radiation_paper

Scripts associated with our radiation manuscript (https://doi.org/10.1101/2022.07.29.501997)

regionalenrichment-nf

Nextflow pipeline to conduct mutational regional enrichment analysis

s2_fpdb-nf

Run a strelka2 variant calling from public data bases, with a step of BAM downloading

samtools-merge-nf

Merge BAM files using samtools

simulatelowcovseq-nf

Nextflow pipeline to simulate low coverage WES from existing BAM files and call/annotate variants with Strelka2

skatmutqtl-nf

Run the SKAT-O rare variant method for the mutQTL identification

snps-prs

nextflow pipeline to compute PolygenicRiskScores for driver genes

snv_clusters_sig-nf

Compute mutational signatures from clusters of SNVs

strelka2-nf

sv-simulation-nf

Nextflow pipeline to simulate structural variations in long reads sequencing data

talks

Repository for beamer presentations

tp_bioinfo_l3_genomique

variant-filtering-kidney2hits

R scripts to filter variants from germline needlestack calling

variantfiltering-nf

nextflow pipeline to perform variant filtering on NGS data

vcf-tips-tricks

Piece of code to analyse VCF files

vcf_ancestry-nf

Nextflow pipeline that filters a VCF on a given ancestry from a PCA on 1000 genomes