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Bioinformatics Python Packages

Python packages with the GitHub topic bioinformatics. Sorted by relevance, with stars and monthly downloads.
plotly
dash

Data Apps & Dashboards for Python. No JavaScript Required.

9.3M 24K 2K
biopython
biopython

Official git repository for Biopython (originally converted from CVS)

8.4M 5K 2K
biotite-dev
biotite

A comprehensive library for computational molecular biology

4.6M 944 136
althonos
pyhmmer

Cython bindings and Python interface to HMMER3.

3.1M 162 17
scverse
anndata

Annotated data.

2.1M 736 191
pysam-developers
pysam

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

1.7M 889 297
mdshw5
pyfaidx

Efficient pythonic random access to fasta subsequences

906K 485 76
scverse
scanpy

Single-cell analysis in Python. Scales to >100M cells.

824K 2K 741
danielchen05
spotsweeper

Spatially-aware quality control for spatial transcriptomics

539K 9 0
owkin
pydeseq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

506K 748 83
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

280K 62 41
PDBeurope
pdbeccdutils

A set of python tools to deal with PDB chemical components definitions for small molecules, taken from the wwPDB Chemical Component Dictionary, uses RDKit

271K 79 12
brentp
cyvcf2

cython + htslib == fast VCF and BCF processing

209K 440 76
Martinsos
edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

201K 591 172
pepkit
peppy

Project metadata manager for PEPs in Python

175K 40 13
databio
piper

Python toolkit for building restartable pipelines

132K 47 9
mims-harvard
pytdc

Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science

131K 1K 211
ga4gh
ga4gh

A reference implementation of the GA4GH API

121K 99 91
marcelm
dnaio

Efficiently read and write sequencing data from Python

117K 70 9
scikit-bio
scikit-bio

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

107K 1K 328
tskit-dev
tskit

Population-scale Ancestral Recombination Graph (ARG) library

97K 183 83
galaxyproject
galaxy-tool-util

Data intensive science for everyone.

91K 2K 1K
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