Gwas Python Packages

hail

Cloud-native genomic dataframes and batch computing

pycmplot

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

sgkit

Scalable genetics toolkit

magenpy

Modeling and Analysis of Statistical Genetics data in python

gwaspeek

gwaspeek: interactive terminal viewer for GWAS summary statistics

qmplot

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

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.

variant-spark

machine learning for genomic variants

viprs

Variational Inference of Polygenic Risk Scores (VIPRS)

gentropy

Open Targets python framework for post-GWAS analysis

gsmap

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

gps-mapping

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

easyfinemap

user-friendly pipeline for GWAS fine-mapping

zorp

A simple GWAS parser + CLI

scoary

Pan-genome wide association studies

pysumstats

Python package for reading, combining, meta-analyzing, and saving GWAS summary statistics data.

j11hail

Cloud-native genomic dataframes and batch computing

haptools

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

panfeed

A k-mer counter that streams gene-cluster specific k-mers, while keeping k-mer positional information. Useful for microbial GWAS analyses with higher interpretability.

haplodynamics

A python library to develop genomic data simulators

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.

cpg-hail

Cloud-native genomic dataframes and batch computing

scdrs

Single-cell disease relevance score (scDRS)

genetest

Python package for efficient genetic association analyses