KEGG Pathway Enrichment (clusterProfiler)

What it does

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.

When to use it

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.

What's included

• Scripts: examples and R code snippets demonstrating enrichKEGG, enrichMKEGG, setReadable, compareCluster, and pathview (in-skill examples; no external scripts detected).
• References: guidance on organism codes, ID conversion, background universe, and notes on KEGG licensing and alternatives.
• Instructions: step-by-step patterns for preparing gene lists, converting IDs, running enrichment with appropriate parameters (pvalue/qvalue, min/max GS size), exporting CSV results, and visualizing pathways.

Compatible agents

Likely used by agents that can run R or provide R guidance and code (Claude Code, Codex/Copilot-style agents with R support).