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 BioTender-max/awesome-bio-agent-skills --skill kegg-pathways --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. # KEGG Pathway Enrichment ## Core Pattern **Goal:** Identify KEGG metabolic and signaling pathways over-represented in a gene list. **Approach:** Test for enrichment using the hypergeometric test via clusterProfiler enrichKEGG against the KEGG online database. **"Find enriched KEGG pathways in my gene list"** → Test whether KEGG pathway gene sets are over-represented among significant genes. ```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 **Goal:** Extract significant Entrez gene IDs from DE results in the format required by enrichKEGG. **Approach:** Filter by significance thresholds and convert gene symbols to Entrez IDs (KEG
- Version Compatibility
- Core Pattern
- Prepare Gene List
- KEGG ID Conversion
- Run KEGG Pathway Enrichment
- Make Results Readable
- KEGG Module Enrichment
- Common Organism Codes
- Background Universe (Critical)
- Extract and Export Results
- Browse KEGG Pathways
- Key Parameters
- Compare Multiple Gene Lists
- Prokaryotic / Non-Model Organism KEGG
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 BioTender-max/awesome-bio-agent-skills --skill kegg-pathways --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.