Pathway Enrichment Analysis Python Packages

pywikipathways

Python Client Package for WikiPathways

kinase-library

The Kinase Library: a Global Atlas of the Human Protein Kinome

sspa

Single sample pathway analysis tools for omics data

pathway-forte

A Python package for benchmarking pathway database with functional enrichment and classification methods

roma-analysis

Representation and Quantification Of Module Activity in Single Cells

genpath-pph

GenPath-PPH: Python package for integrating gene expression and KEGG pathway networks via Persistent Path Homology to detect disease-relevant pathway dysregulation. Available on PyPI: pip install genpath-pph

scroma

Batch-aware SVD-based pathway-activity inference for single-cell transcriptomics

pymean

A Python package for metabolite enrichment analysis.

reactomepy

Explore biomolecular pathways in Reactome from the command-line or a Python script