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hail-is
hail

Cloud-native genomic dataframes and batch computing

88K 1K 264
esohkevin
pycmplot

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

7K 0 0
sgkit-dev
sgkit

Scalable genetics toolkit

5K 275 39
shz9
magenpy

Modeling and Analysis of Statistical Genetics data in python

2K 18 5
ShujiaHuang
qmplot

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

2K 50 10
Cloufield
gwaspeek

gwaspeek: interactive terminal viewer for GWAS summary statistics

2K 2 0
jschnable
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.

2K 15 6
aehrc
variant-spark

machine learning for genomic variants

1K 147 48
opentargets
gentropy

Open Targets python framework for post-GWAS analysis

1K 53 15
shz9
viprs

Variational Inference of Polygenic Risk Scores (VIPRS)

1K 30 3
JianYang-Lab
gsmap

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

914 204 16
LeonSong1995
gps-mapping

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

903 204 16
Jianhua-Wang
easyfinemap

user-friendly pipeline for GWAS fine-mapping

881 14 3
abought
zorp

A simple GWAS parser + CLI

756 1 0
AdmiralenOla
scoary

Pan-genome wide association studies

737 216 34
cast-genomics
haptools

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

707 24 5
hail-is
j11hail

Scalable library for exploring and analyzing genomic data.

610 1K 264
microbial-pangenomes-lab
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.

587 9 0
matthijsz
pysumstats

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

543 3 0
remytuyeras
haplodynamics

A python library to develop genomic data simulators

526 4 0
hail-is
cpg-hail

Cloud-native genomic dataframes and batch computing

439 1K 264
jrazi
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.

431 3 0
pgxcentre
genetest

Python package for efficient genetic association analyses

419 3 2
martinjzhang
scdrs

Single-cell disease relevance score (scDRS)

405 182 23
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