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Genomics Python Packages

Python packages with the GitHub topic genomics. Sorted by relevance, with stars and monthly downloads.
biopython
biopython

Official git repository for Biopython (originally converted from CVS)

8.6M 5K 2K
mdshw5
pyfaidx

Efficient pythonic random access to fasta subsequences

876K 485 76
ga4gh
ga4gh-cat-vrs

GA4GH Categorical Variation Representation Python Implementation

308K 2 5
ga4gh
ga4gh-va-spec

GA4GH Variation Annotation Python Implementation

303K 2 1
ga4gh
ga4gh-vrs

GA4GH Variation Representation Python Implementation

281K 62 41
brentp
cyvcf2

cython + htslib == fast VCF and BCF processing

209K 440 76
scverse
mudata

Multimodal Data (.h5mu) implementation for Python

151K 120 22
ga4gh
ga4gh

A reference implementation of the GA4GH API

121K 99 91
tskit-dev
tskit

Population-scale Ancestral Recombination Graph (ARG) library

98K 183 83
hail-is
hail

Cloud-native genomic dataframes and batch computing

92K 1K 264
biocommons
bioutils

provides common tools and lookup tables used primarily by the hgvs and uta packages

89K 25 20
galaxyproject
galaxy-tool-util

Data intensive science for everyone.

89K 2K 1K
galaxyproject
galaxy-util

Data intensive science for everyone.

88K 2K 1K
tskit-dev
msprime

Simulate ARGs and genomic sequence data using population genetic models

85K 214 92
biocommons
biocommons-seqrepo

non-redundant, compressed, journalled, file-based storage for biological sequences

80K 50 36
galaxyproject
galaxy-tool-util-models

Data intensive science for everyone.

77K 2K 1K
biocommons
hgvs

Python library to parse, format, validate, normalize, and map sequence variants according to HGVS Nomenclature (https://hgvs-nomenclature.org/).

72K 287 97
pyranges
pyranges

Performant Pythonic GenomicRanges

67K 495 50
biocommons
eutils

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

54K 64 29
tanghaibao
goatools

Python library to handle Gene Ontology (GO) terms

45K 886 213
pachterlab
gget

🧬 gget enables efficient querying of genomic reference databases

40K 1K 85
genomoncology
biomcp-python

BioMCP: Biomedical Model Context Protocol

39K 500 101
open2c
bioframe

Genomic interval operations on Pandas DataFrames

33K 191 35
cogent3
cogent3

Comparative Genomics Toolkit 3

25K 134 67
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