Genetics Python Packages

msprime

Simulate ARGs and genomic sequence data using population genetic models

hail

Cloud-native genomic dataframes and batch computing

splicecraft

In-Terminal Plasmid Design Workbench

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

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

adamixture

Fast population clustering with Adam-EM Optimization.

lineage

tools for analyzing and exploring genetic relationships

mehari

Python bindings for the mehari variant annotator

mixalime

Identification of allele-specific events in sequencing experiments.

vencode

Package to get VEnCodes as in Macedo and Gontijo, 2019

natal-core

Numba-Accelerated Toolkit for Analysis of Lifecycles

cai

Python implementation of codon adaptation index

cutevariant

GUI to visualize and process variant data

varfish-cli

Command line interface client for VarFish Server.

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.

mutalyzer-algebra

A Boolean Algebra for Genetic Variants

gentropy

Open Targets python framework for post-GWAS analysis

pyplink

Python module to read binary Plink files.

doublehelix

Genomic data manipulation tool

trifusion

Streamlining phylogenomic data gathering, processing and visualization