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artemisia

Perl tools for hacking genomic data

barrys_conda_envs

Conda environments repository for Barry Moore

c_sandbox

A repo for playing with C code

catherpes

Python tools for hacking genomic data

cercocarpus

Python tools for hacking text data

cirque

Perl tools for hacking on text data

cruzdb

python access to UCSC genomes database

farmhand

FarmHand provides a perl interface to the MPI library allowing you to write perl scripts that can execute a function on multiple data points in parallel in an MPI environment with minimal interaction with (or understanding of) MPI specific code.

gffutils

GFF and GTF file manipulation and interconversion

gvcf_pipeline-nf

Nextflow pipeline for generate GVCF from BAM with GenomeAnalysisTK with step of realignment

hap.py

Haplotype VCF comparison tools

hts-python

pythonic wrapper for htslib

leafcutter

Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard

mm-github-pages-starter

Minimal Mistakes GitHub Pages site starter

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

multiqc_testdata

Test data for MultiQC. See https://github.com/ewels/MultiQC

nirvana

The nimble & robust variant annotator

oneliners

Useful bash one-liners for bioinformatics.

phenven

pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl

pyfaidx

Efficient pythonic random access to fasta subsequences

pyfastx

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

sandbox

slate

Slate is a Jekyll theme for GitHub Pages

spikely

A tool for spiking pathogenic alleles into a VCF file for testing disease gene/variant prioritization tools