Gwas Python Packages

hail

Cloud-native genomic dataframes and batch computing

36K 1K 267

jamma

JAMMA (Highly-Accelerated Multi-method Mixed-model Association) -- a fast and modern Python and C reimplementation of GEMMA for large-scale GWAS.

17K 3 1

pylocuszoom

pyLocusZoom -- publication-ready GWAS visualization in Python: LocusZoom-style regional association plots with LD coloring, gene tracks and recombination overlays, plus Manhattan, QQ, Miami, eQTL, fine-mapping, PheWAS and forest plots. Dog and cat genomes built in.

5K 2 0

magenpy

Modeling and Analysis of (Statistical) Genetics data in python

5K 22 5

sgkit

Scalable genetics toolkit

4K 285 42

snputils

Python toolkit for fast genotype I/O, ancestry analysis, population-genetics statistics, genotype QC, GWAS, and visualization

3K 54 4

janusx

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

3K 41 7

viprs

Variational Inference of Polygenic Risk Scores

3K 36 4

pygapit-ng

Python implementation of GAPIT 3.5 for GWAS and genomic prediction, with disk-backed NumPy, HDF5, and Zarr workflows.

2K 0 0

pycmplot

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

2K 6 1

sushie

Software to perform multi-ancestry SNP fine-mapping on molecular data

1K 34 8

gentropy

Open Targets python framework for post-GWAS analysis

1K 59 17

scoary

Pan-genome wide association studies

975 226 35

gsmap

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

740 223 18

biosuite-ultra

Integrated pure-Python bioinformatics platform: 47 analysis modules, 105 plotting functions, molecular cloning with 169 restriction enzymes, and reproducible workflows through Python, CLI, GUI, and REST API.

648 6 3