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 majiayu000/claude-skill-registry --skill 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.
# GO Over-Representation Analysis ## Core Pattern ```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 adjustment method pvalueCutoff = 0.05, qvalueCutoff = 0.2 ) ``` ## Prepare Gene List from DE Results ```r library(dplyr) de_results <- read.csv('de_results.csv') sig_genes <- de_results %>% filter(padj < 0.05, abs(log2FoldChange) > 1) %>% pull(gene_id) # If using gene symbols, convert to Entrez IDs gene_ids <- bitr(sig_genes, fromType = 'SYMBOL', toType = 'ENTREZID', OrgDb = org.Hs.eg.db) gene_list <- gene_ids$ENTREZID ``` ## ID Conversion with bitr ```r # Check available key types keytypes(org.Hs.eg.db) # Convert between ID types converted <- bitr(genes, fromType = 'ENSEMBL', toType = 'ENTREZID', OrgDb = org.Hs.eg.db) # Multiple output types converted <- bitr(genes, fromType = 'SYMBOL', toType = c('ENTREZID', 'ENSEMBL'), OrgDb = org.Hs.eg.db) ``` ## With Background Universe ```r # Use all expressed g
- 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 majiayu000/claude-skill-registry --skill 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 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.