Version Compatibility

Reference examples tested with: clusterProfiler 4.18+, org.Hs.eg.db 3.18+, gson 0.1+ (snapshot pinning), SPIA 2.50+ and graphite 1.56+ (topology section).

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 is a LIVE DATABASE, not a package. enrichKEGG/enrichMKEGG/gseKEGG query the KEGG REST API (https://rest.kegg.jp/) at call time, so the same code on the same genes returns DIFFERENT pathways months apart as KEGG updates. For any reported result, pin the release with a gson snapshot (below) and record the access date; use_internal_data=TRUE does NOT pin the current KEGG (it loads the deprecated 2012 KEGG.db).

KEGG Pathway and Topology Enrichment

"Which KEGG pathways are perturbed in my data?" -> Join genes to KEGG's curated pathway/module gene sets (ORA or GSEA), or propagate fold-changes through KEGG's signed wiring (SPIA) - and pin the KEGG release, because the result is a timestamped query against a moving curation, not a fact about the biology.

• R: enrichKEGG(gene, organism, keyType) | gseKEGG(geneList, organism) | spia(de, all, organism)

Scope: KEGG-specific enrichment across all three generations - membership ORA (enrichKEGG/enrichMKEGG), ranked GSEA (gseKEGG), and signed-topology perturbation (SPIA/graphite). KEGG ID mapping (organism codes, keyType, bitr_kegg, prokaryotic locus tags, KO routing), reproducibility/pinning, and pathview map overlay live here. The hypergeometric test and the universe problem -> go-enrichment. The GSEA running-sum engine and ranking-metric choice -> gsea. Reactome/WikiPathways gene sets -> reactome-pathways, wikipathways. Generic dot/cnet/emap plots -> enrichment-visualization. The DE list and fold-changes -> differential-expression/de-results.