Necessary notebook/scripts to run the analysis described in the manuscript.

Variant calling pipeline for yeast samples

IQ-TREE software version 2: phylogenetics by maximum likelihood

A tool to identify and annotate homoplasies on a phylogeny and sequence alignment

A WDL, CWL and Python API supporting easy-to-use workflow engine. It is scalable, efficient and cross-platform (Linux/macOS).

Edit your Jupyter notebooks in Vim/Neovim

calculates tajima's D from bcftools query input

A computational tool for processing and differentiating PCR duplicates from biological duplicates

Toolkit for processing sequences in FASTA/Q formats

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

Data workflow tool, like a "Make for data"

Code for "A direct approach to estimating false discovery rates conditional on covariates" by SM Boca and JT Leek

An awk-like VCF parser

lumpy: a general probabilistic framework for structural variant discovery

Long-read validation of BEDPE structural variation

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It u…

Pilon is an automated genome assembly improvement and variant detection tool

Code snippets for phenotype and genotype simulations...

🔬 Path to a free self-taught education in Bioinformatics!

A Grammar of Animated Graphics

Correlation conditional analysis.

Fast, integrative colocalisation mapping with functional data

Pariwise analysis of GWAS

Functional genomics and genome-wide association studies

NOT YET: Python's excellent ArgumentParser in C++

Enhancements to Heatmap.2 from the gplots R package

Fast, integrative fine mapping with functional data

A Python interface to the BEDTools API using Cython