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.

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

Code and simulations using biologically annotated neural networks

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

A high-performance, ALL-in-ONE suite for quantitative genetics that unifies genome-wide association studies (GWAS) and genomic selection (GS).

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

A faster lmm for GWAS. Supports GPU backend.

The multivariate MArginal ePIstasis Test

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

Higher-order genetic interaction discovery with network-based biological priors.

Code and simulations using interaction-LD score regression

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)

Make interactive LocusZoom plots from a local GWAS file

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

MendelianRandomization is an R package for assessing causal relationships using genetic variants as instrumental variables

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

Coupled Mixed Model

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

Code and simulations using an Ensemble of Single-Effect Neural Networks (ESNN)

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/

Mult-Loci nonlinear/Linear Model based on new algorithm For GWAS , Epistasis and GS（ISR）

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

MGflashfm: joint fine-mapping of genetic association signals in several traits amongst multiple population groups.

A fast and scalable method to detect epistasis in complex traits from biobank-scale studies

mvtests: a suite of functions for testing genetic associations of multiple traits (a.k.a. cross-phenotype associations)

A phylogenetically-aware framework for detecting evolutionary associations between binary traits