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

annnet

A Python tool to build, manipulate, and interoperate with flexible graph structures

spycone

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

favapy

Functional Associations using Variational Autoencoders

bio2bel-entrez

A Bio2BEL package for converting Entrez and HomoloGene to BEL

neet

Simulating and analyzing network models

hbp-knowledge

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

drug2ways

A Python package for drug discovery by analyzing causal paths on multiscale networks

pybel-cx

A PyBEL extension for interconversion with CX

bel2scm

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

bio2bel-drugbank

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

bio2bel-interpro

A Bio2BEL package for converting InterPro to BEL

pathme-viewer

A web application for visualizing and exploring pathway knowledge in Biological Expression Language (BEL)

bio2bel-expasy

A Bio2BEL package for converting ExPASy to BEL

neuropull

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

bel-commons

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

bio2bel-go

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

conib

Curation of Neurodegeneration in Biological Expression Language (CONIB)

hemekg

Modeling heme pathogenicity and pathway dysregulation in the context of hemolytic disorders