This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.

Application for making ENCODE Blacklists

Genomic coordinates of problematic genomic regions as GRanges

This Snakemake pipeline implements the GATK best-practices workflow

ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).

RNA-seq workflow using STAR and DESeq2

🔧 .files, including ~/.macos — sensible hacker defaults for macOS