Gwas Python Packages

hail

Cloud-native genomic dataframes and batch computing

sgkit

Scalable genetics toolkit

janusx

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

magenpy

Modeling and Analysis of (Statistical) Genetics data in python

gentropy

Open Targets python framework for post-GWAS analysis

pyicare

A Python distribution of iCARE, a tool for individualized Coherent Absolute Risk Estimation.

pycmplot

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

gsmap

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

haptools

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

viprs

Variational Inference of Polygenic Risk Scores

easyfinemap

user-friendly pipeline for GWAS fine-mapping.

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.

edgemap

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

scdrs

Single-cell disease relevance score (scDRS)

gps-mapping

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

scoary

Pan-genome wide association studies

qmplot

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

haplodynamics

A python library to develop genomic data simulators

variant-spark

VariantSpark Python API

gwaspeek

gwaspeek: interactive terminal viewer for GWAS summary statistics

genetest

Python package for efficient genetic association analyses

pysumstats

Package for working with GWAS summary statistics

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.

genepi

A package for detecting epistasis by machine learning