bio-pathway-go-enrichment
Gene Ontology over-representation analysis using clusterProfiler enrichGO. Use when identifying biological functions enriched in a gene list from differential expression or other analyses. Supports all three ontologies (BP, MF, CC), multiple ID types, and customizable statistical thresholds.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pathway-go-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.
## Version Compatibility Reference examples tested with: R stats (base), clusterProfiler 4.10+ Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # GO Over-Representation Analysis ## Core Pattern **Goal:** Identify enriched Gene Ontology terms in a gene list from differential expression or similar analyses. **Approach:** Test for over-representation of GO terms using the hypergeometric test via clusterProfiler enrichGO. **"Run GO enrichment on my gene list"** → Test whether biological process, molecular function, or cellular component terms are over-represented among significant genes. ```r library(clusterProfiler) library(org.Hs.eg.db) # Human - change for other organisms ego <- enrichGO( gene = gene_list, # Character vector of gene IDs OrgDb = org.Hs.eg.db, # Organism annotation database keyType = 'ENTREZID', # ID type: ENSEMBL, SYMBOL, ENTREZID, etc. ont = 'BP', # BP, MF, CC, or ALL pAdjustMethod = 'BH', # p-value adjust
- Version Compatibility
- Core Pattern
- Prepare Gene List from DE Results
- ID Conversion with bitr
- With Background Universe
- All Three Ontologies
- Make Results Readable
- Extract and Export Results
- Simplify Redundant Terms
- Different Organisms
- Group GO Terms by Ancestor
- Key Parameters
- Related Skills
What does the bio-pathway-go-enrichment skill do?
Gene Ontology over-representation analysis using clusterProfiler enrichGO. Use when identifying biological functions enriched in a gene list from differential expression or other analyses. Supports all three ontologies (BP, MF, CC), multiple ID types, and customizable statistical thresholds.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pathway-go-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 FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 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.