Genetics Python Packages

hail

Cloud-native genomic dataframes and batch computing

msprime

Simulate ARGs and genomic sequence data using population genetic models

cellrank

CellRank: dynamics from multi-view single-cell data

fwdpy11

Forward-time simulation in Python using fwdpp

gene-normalizer

Services and guidelines for normalizing genes

lzgraphs

LZ76 Graphs and Applications in Immunology

sgkit

Scalable genetics toolkit

cmappy

Assorted tools for interacting with .gct, .gctx files and other Connectivity Map (Broad Institute) data/tools

adamixture

Fast population clustering with Adam-EM Optimization.

mixalime

Mixture Models for Allelic Imbalance Estimation

lineage

tools for analyzing and exploring genetic relationships

natal-core

Numba-Accelerated Toolkit for Analysis of Lifecycles

mehari

Python bindings for the mehari variant annotator

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.

vencode

Package to get VEnCodes as in Macedo and Gontijo, 2019

gentropy

Open Targets python framework for post-GWAS analysis

varfish-cli

Command line interface client for VarFish Server.

pyplink

Python module to read binary Plink files.

cutevariant

A standalone and free application to explore genetics variations from VCF file

gpmap

A Python API for managing genotype-phenotype map data

cai

Python Implementation of Codon Adaption Index

gnomad-db

Scalable SQLite database for fast querying of gnomAD variant annotations (allele frequency, depth, population metrics). Supports gnomAD v2-v4, WGS and WES.

geneparse

A suite of parse for genotype formats.

trifusion

Streamlining phylogenomic data gathering, processing and visualization