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Computational Biology Python Packages

Python packages with the GitHub topic computational-biology. Sorted by relevance, with stars and monthly downloads.
biotite-dev
biotite

A comprehensive library for computational molecular biology

4.7M 950 135
scikit-bio
scikit-bio

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

107K 1K 330
opencobra
cobra

COBRApy is a package for constraint-based modeling of metabolic networks.

58K 560 233
rasbt
biopandas

Working with molecular structures in pandas DataFrames

39K 751 117
biosimulators
biosimulators-utils

Utilities for building standardized command-line interfaces for biosimulation software packages

9K 4 6
gyorilab
indra

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

9K 211 77
myokit
myokit

Source code, issues, and discussions for Myokit: A tool for cardiac electrophysiology modelling and simulation

5K 45 9
adibvafa
codontransformer

CodonTransformer (2M+ Downloads); The tool for codon optimization, optimizing DNA for protein expression

5K 211 31
flamehaven01
stem-ai

Rubric-based trust evaluator for bio/medical AI repositories with dual-path evidence, governance overlay, and institutional audit outputs.

5K 1 0
a-r-j
graphein

Protein Graph Library

4K 1K 141
BojarLab
glycowork

Package for processing and analyzing glycans and their role in biology.

4K 91 19
biosimulators
biosimulators-test-suite

Tools for validating that biosimulation tools are consistent with the BioSimulators standards

4K 7 2
epifluidlab
finaletoolkit

FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.

3K 37 17
albertyw
itolapi

Python API for the Interactive Tree of Life (iTOL)

3K 38 11
cafferychen777
chatspatial

MCP server for spatial transcriptomics analysis through natural language interfaces.

3K 37 9
alondmnt
codon-bias

Python package of codon usage bias analysis tools

3K 21 9
SED-ML
kisao

Ontology of algorithms for analyzing biological models, their parameters, and their outputs

3K 12 0
wowcowdowjones
proteinfp

End-to-end protein function prediction from structure alone: active sites, binding pockets, GO terms, PPI partners, and drug candidates.

2K 4 0
broadinstitute
tangram-sc

Spatial alignment of single cell transcriptomic data.

2K 365 64
trytoolchest
toolchest-client

Toolchest Python client

2K 15 0
akensert
molgraph

Graph neural networks for molecular machine learning: Implemented and compatible with TensorFlow and Keras.

2K 64 5
biosimulators
biosimulators-copasi

BioSimulators-compliant command-line interface to the COPASI simulation program <http://copasi.org>.

2K 2 3
biomass-dev
biomass

A Python Framework for Modeling and Analysis of Signaling Systems

2K 29 13
biosimulators
biosimulators-tellurium

BioSimulators-compliant command-line interface to the Tellurium/roadrunner simulator <https://tellurium.readthedocs.io/>.

2K 2 2
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