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()