Genetics Python Packages

hail

Cloud-native genomic dataframes and batch computing

msprime

Simulate ARGs and genomic sequence data using population genetic models

splicecraft

Terminal-based plasmid map viewer, sequence editor, and cloning/mutagenesis workbench in pure Python

bgen-limix

A BGEN file format reader library with python bindings. Maintained fork of limix/bgen and cbgen

fwdpy11

Forward-time simulation in Python using fwdpp

natal-core

Numerical Aggregation Toolkit for Analysis of Lifecycles

cellrank

CellRank: dynamics from multi-view single-cell data

adamixture

Fast population genetics clustering.

lzgraphs

Alignment-free graph models of TCR and BCR repertoires built from Lempel-Ziv and FlashBack string decompositions. Compute sequence generation probability (Pgen) and repertoire diversity, and generate new sequences. Python with a C core.

cmappy

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

sgkit

Scalable genetics toolkit

gene-normalizer

Services and guidelines for normalizing genes

snputils

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

genoio

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

sushie

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

sceps

scEPS integrates GWAS and single-cell disease cell atlas data to identify disease-associated cell neighborhoods.

mehari

VEP-like tool for sequence ontology and HGVS annotation of VCF files

mixalime

Mixture Models for Allelic Imbalance Estimation

gentropy

Open Targets python framework for post-GWAS analysis

gpmap

A Python API for managing genotype-phenotype map data

epistasis

A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.

lineage

tools for analyzing and exploring genetic relationships

pyplink

Python module to read binary Plink files.

vencode

Package to get VEnCodes as in Macedo and Gontijo, 2019