Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)

Gene set variation analysis

pathfindR: Enrichment Analysis Utilizing Active Subnetworks

CAusal Reasoning for Network Identification with integer VALue programming in R

Lightweight Iterative Gene set Enrichment in R

Explore the cancer relevance of your gene list

From RNA-seq raw reads to enriched pathways by DEGs

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

Analysis and visualization of RNA-Seq results

Python Client Package for WikiPathways

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

Single sample pathway analysis tools for omics data

A Python package for metabolite enrichment analysis.

FunMappOne: a tool to summarize and visually navigate functional categories in multiple experiments.

R package for de novo pathway enrichment using KeyPathwayMiner

Cellular​ ​signatures​ characterisation ​after​ ​carcinogenic​ ​chemical​ ​exposure​ ​in​ ​mammalian​ ​tissue.

WikiPathways Database

GWAS of Postmortem Brain Samples Sheds Light on the Development of Schizophrenia and Bipolar Disorder

WikiPathways Summit Planning

Curated list of analysis pipelines for biological & clinical interpretation of data-driven findings