Packages
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networkx
NetworkX provides data structures and…
permissive · active · 290.9M/mo
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biopython
Biopython provides Python tools for…
unclear · active · 14.4M/mo
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firecrawl-py
Client library for the Firecrawl API that…
permissive · active · 7.3M/mo
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intervaltree
A self-balancing interval tree data structure…
permissive · aging · 6.3M/mo
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albumentations
Albumentations applies image transformations to…
permissive · aging · 5.5M/mo
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PubChemPy
PubChemPy is a Python wrapper around the…
permissive · aging · 5.4M/mo
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simsimd
SimSIMD provides SIMD-optimized kernels for…
permissive · active · 3.8M/mo
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igraph
igraph provides a Python interface to a…
copyleft · active · 3.4M/mo
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biotite
Biotite provides a unified Python library for…
permissive · active · 3.3M/mo
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biotraj
Reads and writes molecular dynamics trajectory…
copyleft · aging · 2.2M/mo
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anndata
anndata handles annotated data matrices in…
permissive · active · 1.8M/mo
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pyhmmer
PyHMMER provides Python bindings to HMMER3, a…
permissive · active · 1.6M/mo
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firecrawl
A Python SDK for web scraping, crawling,…
permissive · active · 1.5M/mo
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biothings-client
biothings_client provides Python wrappers to…
permissive · active · 1.5M/mo
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mygene
Mygene is a Python wrapper for the MyGene.Info…
permissive · dormant · 1.5M/mo
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gprofiler-official
Python interface to g:Profiler toolkit for…
permissive · abandoned · 1.4M/mo
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gemmi
Gemmi is a C++ library with Python bindings for…
copyleft · active · 1.1M/mo
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scanpy
Scanpy is a toolkit for preprocessing,…
permissive · active · 1.0M/mo
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pgmpy
pgmpy provides data structures and algorithms…
unclear · active · 957.9K/mo
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planarity
Tests whether a graph is planar, computes…
permissive · active · 709.6K/mo
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pybigtools
pybigtools is a Python wrapper around a Rust…
permissive · active · 636.4K/mo
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python-igraph
Python interface to the igraph graph library…
copyleft · active · 596.7K/mo
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pyfaidx
Provides fast random access to subsequences in…
permissive · active · 529.9K/mo
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numkong
NumKong provides mixed-precision linear algebra…
permissive · active · 496.0K/mo
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propka
PROPKA predicts pKa values of ionizable groups…
copyleft · dormant · 436.8K/mo
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primer3-py
primer3-py wraps the Primer3 library to provide…
copyleft · active · 435.4K/mo
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mrcfile
mrcfile reads and writes MRC2014 format files…
permissive · active · 434.1K/mo
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pdb2pqr
PDB2PQR prepares protein structures from PDB…
permissive · active · 430.2K/mo
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mmcif-pdbx
Provides a pure Python interface to read,…
permissive · active · 429.4K/mo
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py3Dmol
Embeds an interactive 3D molecular viewer in…
permissive · active · 427.3K/mo
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alchemlyb
alchemlyb parses molecular dynamics simulation…
permissive · active · 392.9K/mo
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vesin
Vesin computes neighbor lists for atomistic…
permissive · active · 351.7K/mo
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prefixmaps
Retrieves and manages semantic prefix maps that…
permissive · active · 328.0K/mo
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prefixcommons
Converts between CURIEs (compact URI…
permissive · dormant · 307.2K/mo
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json-flattener
Converts nested JSON/YAML objects into flat…
permissive · dormant · 301.8K/mo
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pycat-napari
PyCAT-Napari is a napari-based desktop…
permissive · active · 297.0K/mo
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cwltool
cwltool is the reference implementation of the…
permissive · active · 294.7K/mo
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pyteomics
Pyteomics provides Python tools for proteomics…
permissive · active · 286.4K/mo
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openslide-python
OpenSlide Python provides a Python interface to…
copyleft · active · 270.4K/mo
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vesin-torch
Computes neighbor lists for atomistic systems…
permissive · active · 263.6K/mo
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MDAnalysis
MDAnalysis reads and analyzes molecular…
copyleft · active · 256.7K/mo
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gseapy
Performs gene set enrichment analysis (GSEA) on…
permissive · active · 249.9K/mo
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pdbeccdutils
Parse and process small molecule definitions…
permissive · active · 238.7K/mo
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ubiquerg
Ubiquerg provides a collection of low-level…
permissive · active · 237.7K/mo
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mdtraj
MDTraj reads, writes, and analyzes molecular…
copyleft · active · 221.1K/mo
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cyvcf2
cyvcf2 is a Cython wrapper around htslib that…
permissive · active · 217.2K/mo
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latch
Latch SDK is a framework for building,…
unclear · active · 216.4K/mo
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yacman
Yacman provides a Python interface for reading,…
permissive · active · 213.4K/mo
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refgenconf
Manages standardized configuration for…
permissive · active · 205.0K/mo
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mudata
MuData is a container for multimodal omics data…
permissive · active · 194.2K/mo
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napari
napari is an interactive, multi-dimensional…
permissive · active · 189.5K/mo
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napari-plugin-engine
A plugin discovery and hook-calling system for…
permissive · abandoned · 180.7K/mo
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pymzml
pymzml parses mzML mass spectrometry data files…
permissive · active · 166.3K/mo
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bioblend
BioBlend provides a Python client library for…
permissive · active · 163.6K/mo
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logomaker
Logomaker creates customized sequence…
permissive · aging · 155.3K/mo
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pyxDamerauLevenshtein
Computes Damerau-Levenshtein edit distance…
permissive · active · 153.5K/mo
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bx-python
bx-python provides Python classes and utilities…
permissive · active · 145.7K/mo
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scikit-bio
scikit-bio provides data structures,…
permissive · active · 143.1K/mo
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pronto
Pronto parses, browses, creates, and exports…
permissive · aging · 142.9K/mo
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biom-format
Reads, writes, and manipulates Biological…
permissive · aging · 134.2K/mo
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fastobo
Parses, loads, edits, and serializes OBO (Open…
permissive · aging · 122.5K/mo
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logmuse
Adds standard CLI logging options…
permissive · active · 122.4K/mo
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pysylph
Pysylph provides Python bindings to sylph,…
permissive · dormant · 119.0K/mo
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pephubclient
PEPHubClient provides a Python API and…
permissive · active · 118.1K/mo
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peppy
peppy reads and manages Portable Encapsulated…
permissive · active · 117.9K/mo
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fastpdb
fastpdb is a Rust-based drop-in replacement for…
permissive · abandoned · 117.7K/mo
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fastcluster
Performs fast hierarchical agglomerative…
copyleft · aging · 116.6K/mo
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eido
Validates project metadata against PEP schemas…
permissive · active · 115.5K/mo
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openbabel-wheel
Provides prebuilt Python wheels for OpenBabel,…
copyleft · active · 113.0K/mo
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pybedtools
Wraps the BEDTools suite to perform genomic…
permissive · aging · 109.6K/mo
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ViennaRNA
ViennaRNA provides Python bindings to a C…
unclear · active · 109.3K/mo
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easydev
Provides a collection of utility functions and…
permissive · active · 109.3K/mo
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isa-rwval
Provides Python classes and utilities to read,…
unclear · aging · 107.5K/mo
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pipestat
Pipestat provides a standard API for reporting,…
permissive · active · 105.8K/mo
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mhctools
Unified Python interface to multiple MHC…
permissive · active · 105.8K/mo
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openslide-bin
Provides prebuilt OpenSlide binaries for Linux,…
copyleft · active · 105.4K/mo
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piper
Pypiper manages shell command execution within…
permissive · active · 104.7K/mo
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pyensembl
PyEnsembl provides a Python interface to query…
permissive · active · 104.2K/mo
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datamol
Datamol provides a pythonic layer on top of…
permissive · active · 104.0K/mo
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tiledbsoma
TileDB-SOMA is a Python implementation of the…
permissive · active · 100.8K/mo
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ete3
ETE3 reconstructs, manipulates, analyzes, and…
copyleft · active · 100.4K/mo
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scvi-tools
scvi-tools provides probabilistic models for…
permissive · active · 98.6K/mo
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refgenie
Refgenie manages standardized folder structures…
permissive · active · 97.2K/mo
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varcode
Varcode loads and analyzes genomic variant…
permissive · active · 96.7K/mo
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fabio
FabIO reads and writes 2D X-ray detector images…
permissive · active · 96.1K/mo
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dnaio
dnaio reads and writes FASTQ, FASTA, and uBAM…
permissive · aging · 92.4K/mo
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cobra
COBRApy is a constraint-based modeling package…
copyleft · active · 91.1K/mo
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pygad
PyGAD is a Python library for building and…
unclear · active · 90.1K/mo
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bermuda
Provides Rust-accelerated triangulation…
permissive · active · 85.3K/mo
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multiqc
MultiQC scans bioinformatics analysis…
copyleft · active · 83.2K/mo
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habanero
habanero is a low-level Python client for the…
permissive · active · 83.2K/mo
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napari-plugin-manager
Provides a graphical interface for discovering,…
permissive · active · 82.8K/mo
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prolif
ProLIF generates interaction fingerprints from…
permissive · active · 77.3K/mo
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cellxgene-census
Provides a Python API to query and retrieve…
permissive · active · 76.9K/mo
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gtfparse
Parses GTF (gene transfer format) files into…
permissive · active · 74.3K/mo