from bioskills474
Run KEGG pathway and module enrichment using clusterProfiler (enrichKEGG/enrichMKEGG) to find metabolic and signaling pathways over-represented in a gene list.
Performs KEGG pathway and module over-representation analysis using the R package clusterProfiler. It shows how to prepare Entrez gene lists, convert IDs, run enrichKEGG/enrichMKEGG, set an appropriate background universe, and export readable results and pathway images.
Use this skill when you have a list of significant genes (e.g., from differential expression) and want to identify KEGG pathways or modules enriched in that list across human, model organisms, or many prokaryotes. Also useful for comparing enrichment across groups or preparing pathway visualizations.
Likely used by agents that can run R or provide R guidance and code (Claude Code, Codex/Copilot-style agents with R support).
Documentation-only skill for KEGG pathway enrichment using clusterProfiler in R. No scripts to execute. Well-structured with clear code examples, version compatibility warnings, and practical gotchas like background universe specification and the lack of a readable parameter in enrichKEGG. Covers both eukaryotic and prokaryotic workflows.
Clean documentation skill with no executable code. Good coverage of common pitfalls like background universe inflation and KEGG licensing considerations.
