Genetics Python Packages

msprime

Simulate ARGs and genomic sequence data using population genetic models

fwdpy11

Forward-time simulation in Python using fwdpp

splicecraft

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

hail

Cloud-native genomic dataframes and batch computing

cellrank

CellRank: dynamics from multi-view single-cell data

adamixture

Fast population genetics clustering.

cmappy

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

lzgraphs

LZ76 Graphs and Applications in Immunology

sgkit

Scalable genetics toolkit

gene-normalizer

Services and guidelines for normalizing genes

mehari

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

genoio

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

lineage

tools for analyzing and exploring genetic relationships

snputils

A Python library for processing genomes with ease

cai

Python Implementation of Codon Adaption Index

mixalime

Identification of allele-specific events in sequencing experiments.

gentropy

Open Targets python framework for post-GWAS analysis

cutevariant

GUI to visualize and process variant data

gpmap

A Python API for managing genotype-phenotype map data

vencode

Package to get VEnCodes as in Macedo and Gontijo, 2019

pyplink

Python module to read binary Plink files.

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.

varfish-cli

Command line interface client for VarFish Server.

ct-validation

Benchmarking gene-indication evidence against clinical trial outcomes