The EnrichmentMap protocol provides comprehensive background and troubleshooting guidelines for using EnrichmentMap, and uses freely available and frequently updated software, including gProfiler, Gene Set Enrichment Analysis (GSEA), Cytoscape and EnrichmentMap.
The complete protocol can be performed in ~4.5 h and is designed for use by biologists with no prior bioinformatics training.
Please see Pathway enrichment analysis and visualization of omics data using gProfiler, GSEA, Cytoscape and EnrichmentMap for the complete protocol, and The EnrichmentMap Protocol for sample data used in the protocol.