Valentin Marteau's repositories
alpine_workshop
basic rutine to build docker images from alpine base img
atlas_protocol
A computational protocol for atlas-level data integration and analysis as performed in Salcher et al. (2022).
awesome-code-review
An "Awesome" list of code review resources - articles, papers, tools, etc
awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
bd_rhapsody_velocyto
Nextflow workflow to run velocyto.py on BD Rhapsody BAM files
downloader
Easy & parallel download of FASTQ files from public repositories (SRA, EGA, GDC)
nf-bulk-pipeline
nf-pipeline template for custom data analysis, renders report
fetchngs
Pipeline to fetch metadata and raw FastQ files from public and private databases
FriendsDontLetFriends
Friends don't let friends make certain types of data visualization - What are they and why are they bad.
luca
Single-cell Lung Cancer Atlas with 1.2M cells
minimal-nextflow-template
Template repo for minimal nextflow pipelines. Use this instead of manually submitting SGE jobs.
nextflow-patterns
A curated collection of Nextflow implementation patterns -- http://nextflow-io.github.io/patterns/index.html
nf-deseq2
A RNA-seq differential expression analysis pipeline downstream of nf-core/rnaseq.
nmp-liver
Single cell analysis of donor livers pre- and post machine perfusion
scrnaseq
A single-cell RNAseq pipeline for 10X genomics data
sfaira
data and model repository for single-cell data
terminal-mac-cheatsheet
List of my most used commands and shortcuts in the terminal for Mac