Gwas Python Packages

hail

Cloud-native genomic dataframes and batch computing

sgkit

Scalable genetics toolkit

magenpy

Modeling and Analysis of (Statistical) Genetics data in python

pycmplot

Multi-track circular and linear Manhattan plot generation for GWAS summary statistics

viprs

Variational Inference of Polygenic Risk Scores

gentropy

Open Targets python framework for post-GWAS analysis

gps-mapping

Genetics-informed pathogenic spatial mapping

zorp

A simple GWAS parser + CLI

qmplot

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

gsmap

Integrating GWAS and spatial transcriptomics for spatially resolved mapping of cells associated with human complex traits.

gwaspeek

An interactive terminal viewer for GWAS summary statistics that lets you pan, zoom, and inspect Manhattan plots

haplodynamics

A python library to develop genomic data simulators

panicle

Python package for Genome-Wide Association Studies (GWAS). Implements GLM, MLM, FarmCPU, and BLINK with support for VCF, PLINK, HapMap, and CSV genotype formats.

easyfinemap

user-friendly pipeline for GWAS fine-mapping

scdrs

Single-cell disease relevance score (scDRS)

scoary

Pan-genome wide association studies

knockofforigins

A Python implementation of the "Controlling the False Discovery Rate via Knockoffs" paper from 2015, designed to provide tools for generating knockoff features and applying controlled variable selection techniques in high-dimensional data settings.

variant-spark

machine learning for genomic variants

pysumstats

Package for working with GWAS summary statistics

haptools

Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis

j11hail

Cloud-native genomic dataframes and batch computing

cpg-hail

Cloud-native genomic dataframes and batch computing

panfeed

Compute gene-cluster specific k-mers over a pangenome

genetest

Python package for efficient genetic association analyses