Statistical Genetics Python Packages

jamma

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

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.

sgkit

Scalable genetics toolkit

genoio

Minimalist API for parsing genotype files into Numpy data structures, backed by Rust.

pygapit-ng

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

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.

edgemap

Python package for partitioning GWAS heritability into cell-intrinsic (node) and cell-cell communication (edge) components from spatial transcriptomics.