Pathway Analysis Python Packages

reactome2py

python client for reactome content, analysis, and human functional protein interactions (FI) services api calls.

compath-utils

A repository containing abstract classes that Bio2BEL repos should extend to be adapted to the Compath environment

sspa

Single sample pathway analysis tools for omics data

compath-resources

This repository contains the different resources derived or generated using ComPath

pathintegrate

PathIntegrate: multivariate modelling approaches for pathway-based muti-omics integration

bio2bel-msig

Integration of pathway-related information from MSigDB in BEL

sceptr-profiling

Continuous enrichment profiling for transcriptomes. Characterise how functional programmes are distributed across the expression gradient, with built-in significance testing for single samples. Great for non-model organisms, clinical isolates, and unreplicated datasets.

compath

A web application for exploring and comparing the overlaps across pathway resources

pathme

Harmonizing pathway databases using Biological Expression Language (BEL)

gsea-api

Pandas API for multiple Gene Set Enrichment Analysis implementations in Python (GSEApy, cudaGSEA, GSEA)

pygenprop

A python library for programmatic usage of EBI InterPro Genome Properties.

pathme-viewer

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

scvega

VEGA: a VAE Enhanced by Gene Annotations for interpretable scRNA-seq deep learning

compath-hgnc

A wrapper around Bio2BEL HGNC for ComPath