gsea-enrichment-analysis
GSEA and Pathway Enrichment Analysis
Overview
This skill covers gene set enrichment analysis (GSEA) and pathway enrichment workflows in OmicVerse. It provides critical guidance on the correct data formats and API usage patterns to avoid common errors.
Critical API Reference - Geneset Format
IMPORTANT: Use Dictionary Format, NOT File Path!
The ov.bulk.geneset_enrichment() function requires a dictionary of gene sets, NOT a file path string. You must first load the geneset file using ov.utils.geneset_prepare().
CORRECT usage:
# Step 1: Download pathway database (if not already available)
ov.utils.download_pathway_database()
# Step 2: Load geneset file into dictionary format - REQUIRED!
pathways_dict = ov.utils.geneset_prepare(
'genesets/GO_Biological_Process_2021.txt', # or .gmt file
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