gsea-enrichment-analysis

Gene set enrichment analysis identifies biological pathways and functions enriched in your gene list. Load pathway databases (GO, KEGG, Reactome) into a dictionary using ov.utils.geneset_prepare(), then pass it to ov.bulk.geneset_enrichment() with your DEG list. Visualize results to interpret pathway significance.

Gene sets must be loaded as a dictionary, not a file path. OmicVerse accepts .txt, .gmt, or .json files, but ov.utils.geneset_prepare() converts them into the required dictionary format before enrichment analysis.

The common error occurs when passing a file path directly to geneset_enrichment instead of a dictionary. Always call ov.utils.geneset_prepare() first to load and format your gene sets, then pass the resulting dictionary to the enrichment function.

Yes, this workflow supports both Human and Mouse organisms. Download species-specific pathway databases using ov.utils.download_pathway_database(), ensure gene symbols match your organism, and validate the format before running enrichment.

This workflow integrates GO (Gene Ontology), KEGG, Reactome, and related pathway databases. Download available databases for your organism, load them as dictionaries, and run enrichment to identify significant biological processes and pathways.