Networks Biology Python Packages

pybel

🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)

bio2bel-kegg

A Bio2BEL package for integrating pathway-related information from KEGG in BEL

bio2bel-reactome

Integration of pathway-related information from Reactome in BEL

bio2bel-entrez

A Bio2BEL package for converting Entrez and HomoloGene to BEL

favapy

Functional Associations using Variational Autoencoders

annnet

AnnNet (Annotated Network) is a unified, high-expressivity graph platform designed to bring the convenience of AnnData-style annotated containers to networks, multilayer structures, and hypergraphs.

neet

Simulating and analyzing dynamical network models

drug2ways

Reasoning over polar paths in biological networks for drug discovery applications

spycone

Splicing-aware time-course network enricher - exploratory analysis for transcriptomics and/or proteomics time series data

bio2bel-drugbank

A Bio2BEL package for DrugBank (https://www.drugbank.ca)

hbp-knowledge

Knowledge curated in BEL from full text during the Human Brain Pharmacome project

bel2scm

Generate dynamic structural causal models from biological knowledge graphs encoded in the Biological Expression Language (BEL)

pybel-cx

A PyBEL extension for interconversion with CX

bio2bel-interpro

A Bio2BEL package for converting InterPro to BEL

bio2bel-expasy

A Bio2BEL package for converting ExPASy to BEL

bel-commons

An environment for curating, validating, and exploring knowledge assemblies encoded in BEL

pathme-viewer

A plugin for PathMe that allows to explore overlaps across pathway databases

bio2bel-go

A Bio2BEL package for converting the Gene Ontology (GO) to BEL

neuropull

A (soon to be) lightweight Python package for accessing single-cell connectome networks with metadata.

conib

Curation of Neurodegeneration in Biological Expression Language (CONIB)

hemekg

Mechanistic knowledge about heme and hemolytic disorders in Biological Expression Language with PyBEL