gsea-enrichment-analysis
Gene set enrichment analysis with correct geneset format handling. Critical guidance for loading pathway databases and running enrichment in OmicVerse.
npx skills add majiayu000/claude-skill-registry --skill gsea-enrichment --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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:** ```python # 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 organism='Human' # or 'Mouse' ) # Step 3: Now run enrichment with the DICTIONARY enr = ov.bulk.geneset_enrichment( gene_list=deg_genes, pathways_dict=pathways_dict, # Pass the DICTIONARY, not file path! pvalue_type='auto', organism='Human' ) ``` **WRONG - DO NOT USE:** ```python # WRONG! Don't pass file path directly to geneset_enrichment! # enr = ov.bulk.geneset_enrichme
- Overview
- Critical API Reference - Geneset Format
- IMPORTANT: Use Dictionary Format, NOT File Path!
- File Format Support
- Complete Enrichment Workflow
- Common Errors and Solutions
- Error: "FileNotFoundError" or "pathwaysdict is not a dict"
- Error: "Missing file 'genesets/GOBiologicalProcess2021.gmt'"
- Error: "No enriched pathways found"
- Pathway Databases Available
- Best Practices
- Examples
- References
What does the gsea-enrichment-analysis skill do?
Gene set enrichment analysis with correct geneset format handling. Critical guidance for loading pathway databases and running enrichment in OmicVerse.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill gsea-enrichment --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.