vjmarteau Goto Github PK

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

caf-subtype-metabolism

climbing_stats

current-topics-bioinformatics-lecture

downloader

Easy & parallel download of FASTQ files from public repositories (SRA, EGA, GDC)

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.

journal_club_31-05-2022

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-bulk-pipeline

nf-pipeline template for custom data analysis, renders report

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

obsidian-notebook

pas_analysis

scrnaseq

A single-cell RNAseq pipeline for 10X genomics data

scrnaseq-calprotectin-organoids

scrnaseq-gpx4-mouse

sfaira

data and model repository for single-cell data

sparovec_pas

star_protocol

terminal-mac-cheatsheet

List of my most used commands and shortcuts in the terminal for Mac

tutorial_deseq2_contrasts

tyr-ref-back

vjmarteau

Config files for my GitHub profile.