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Genetics Python Packages

Python packages with the GitHub topic genetics. Sorted by relevance, with stars and monthly downloads.
hail-is
hail

Cloud-native genomic dataframes and batch computing

92K 1K 264
tskit-dev
msprime

Simulate ARGs and genomic sequence data using population genetic models

85K 214 92
theislab
cellrank

CellRank: dynamics from multi-view single-cell data

9K 443 57
molpopgen
fwdpy11

Forward-time simulation in Python using fwdpp

8K 32 6
cancervariants
gene-normalizer

Services and guidelines for normalizing genes

8K 3 4
MuteJester
lzgraphs

LZ76 Graphs and Applications in Immunology

8K 6 0
sgkit-dev
sgkit

Scalable genetics toolkit

5K 275 39
cmap
cmappy

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

5K 141 77
AI-sandbox
adamixture

Fast population clustering with Adam-EM Optimization.

4K 23 1
autosome-ru
mixalime

Mixture Models for Allelic Imbalance Estimation

4K 11 1
apriha
lineage

tools for analyzing and exploring genetic relationships

3K 175 28
jyzhu-pointless
natal-core

Numba-Accelerated Toolkit for Analysis of Lifecycles

2K 3 1
varfish-org
mehari

Python bindings for the mehari variant annotator

2K 27 1
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
AndreMacedo88
vencode

Package to get VEnCodes as in Macedo and Gontijo, 2019

1K 0 1
opentargets
gentropy

Open Targets python framework for post-GWAS analysis

1K 53 15
bihealth
varfish-cli

Command line interface client for VarFish Server.

1K 2 2
lemieuxl
pyplink

Python module to read binary Plink files.

931 17 4
labsquare
cutevariant

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

879 108 21
harmslab
gpmap

A Python API for managing genotype-phenotype map data

863 12 8
Benjamin-Lee
cai

Python Implementation of Codon Adaption Index

808 37 11
KalinNonchev
gnomad-db

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

790 52 12
pgxcentre
geneparse

A suite of parse for genotype formats.

725 5 2
ODiogoSilva
trifusion

Streamlining phylogenomic data gathering, processing and visualization

651 89 23
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