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gsea-enrichment-analysis
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/gsea-enrichment
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- 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.
- ov.utils.download_pathway_database().
Source Doc
Excerpt From SKILL.md
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 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'
)
python
Use cases
- Use gsea-enrichment-analysis for single-cell or spatial omics analysis.
- Apply gsea-enrichment-analysis to clustering, integration, or trajectory workflows.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
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