bio-pathway-kegg-pathways
KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. Use when identifying metabolic and signaling pathways over-represented in a gene list. Supports 4000+ organisms via KEGG online database.
npx skills add majiayu000/claude-skill-registry --skill kegg-pathways-gptomics-bioskills-2 --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.
# KEGG Pathway Enrichment ## Core Pattern ```r library(clusterProfiler) kk <- enrichKEGG( gene = gene_list, # Character vector of gene IDs organism = 'hsa', # KEGG organism code pvalueCutoff = 0.05, pAdjustMethod = 'BH' ) ``` ## Prepare Gene List ```r library(org.Hs.eg.db) de_results <- read.csv('de_results.csv') sig_genes <- de_results$gene_id[de_results$padj < 0.05 & abs(de_results$log2FoldChange) > 1] # KEGG requires NCBI Entrez gene IDs (kegg, ncbi-geneid) gene_ids <- bitr(sig_genes, fromType = 'SYMBOL', toType = 'ENTREZID', OrgDb = org.Hs.eg.db) gene_list <- gene_ids$ENTREZID ``` ## KEGG ID Conversion ```r # Convert between KEGG and other IDs kegg_ids <- bitr_kegg(gene_list, fromType = 'ncbi-geneid', toType = 'kegg', organism = 'hsa') # Available types: kegg, ncbi-geneid, ncbi-proteinid, uniprot ``` ## Run KEGG Pathway Enrichment ```r kk <- enrichKEGG( gene = gene_list, organism = 'hsa', keyType = 'ncbi-geneid', # or 'kegg' pvalueCutoff = 0.05, pAdjustMethod = 'BH', minGSSize = 10, maxGSSize = 500 ) # View results head(kk) results <- as.data.frame(kk) ``` ## Make Results Readable ```r # enrichKEGG does NOT have readable parameter - use setReadable library(org.Hs.eg.db) kk_read
- Core Pattern
- Prepare Gene List
- KEGG ID Conversion
- Run KEGG Pathway Enrichment
- Make Results Readable
- KEGG Module Enrichment
- Common Organism Codes
- With Background Universe
- Extract and Export Results
- Browse KEGG Pathways
- Key Parameters
- Compare Multiple Gene Lists
- Notes
- Related Skills
What does the bio-pathway-kegg-pathways skill do?
KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. Use when identifying metabolic and signaling pathways over-represented in a gene list. Supports 4000+ organisms via KEGG online database.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill kegg-pathways-gptomics-bioskills-2 --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.