Pathway Analysis Python Packages

reactome2py

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

4K 36 11

esfex

Integrated framework for Energy System modelling

710 6 0

compath-utils

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

477 0 0

sspa

Single sample pathway analysis tools for omics data

459 16 6

gsea-api

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

396 16 2

compath-resources

This repository contains the different resources derived or generated using ComPath

340 9 1

pathway-forte

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

313 13 6

pathme

Harmonizing pathway databases using Biological Expression Language (BEL)

312 20 2

pathintegrate

PathIntegrate Python package for pathway-based multi-omics data integration

311 19 1

roma-analysis

Representation and Quantification Of Module Activity in Single Cells

269 3 0

bio2bel-msig

Integration of pathway-related information from MSigDB in BEL

265 2 0

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

235 0 0

compath

A web application for exploring, analyzing, and curating pathway databases

234 13 0

pathme-viewer

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

119 6 2

pygenprop

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

110 9 5

compath-hgnc

A wrapper around Bio2BEL HGNC for ComPath

73 0 0

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.

56 6 0

scvega

VEGA: VAE Enhanced by Gene Annotations

53 18 2

reactomepy

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

1 23 4