A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.

A Python package for creating high-quality manhattan and Q-Q plots from GWAS results.

kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.

tips and tricks in genome-wide association studies - a tutorial

A faster lmm for GWAS. Supports GPU backend.

A statistical test of pleiotropic effect of a genetic variant on two traits using GWAS summary statistics

Three bacterial GWAS methods all rolled into one easy-to-use R package

Make interactive LocusZoom plots from a local GWAS file

A curated list (with links) of useful tools for genome-wide association analysis.

Application of the Simple Sum method for testing co-localization of GWAS with any other SNP-level data (e.g. eQTL data)

Coupled Mixed Model

R package to perform data pre-processing for more informative bacterial GWAS

Code and Tutorials for Running the MArginal ePIstasis Test (MAPIT)

Code and simulations using biologically annotated neural networks

Recombines real genomic segments to simulate whole genomes

Flashfm: multi-trait fine-mapping that uses GWAS summary statistics from several traits. Updated and more flexible wrapper functions available at jennasimit.github.io/flashfmZero/

R package 📦 with ggplot2 extensions for GWAS summary statistics (still in 🚧)

Tool for genome wide association studies with Bayesian inference and statistical learning

A Bayesian grouped mixture of regressions model capable of estimating SNP marker effect sizes for multiple outcomes simultaneously