Version Compatibility

Reference examples tested with: clusterProfiler 4.18.4+, org.Hs.eg.db 3.22+ (goseq 1.54+ for the length-bias snippet).

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.

GO annotation lives in the local org.*.eg.db OrgDb and GO.db, both pinned to the Bioconductor release, so a GO ORA is reproducible given the package versions - record packageVersion('org.Hs.eg.db') and packageVersion('GO.db') with results. enrichGO moved no core arguments recently, but several plot helpers migrated to enrichplot in clusterProfiler 4.x (those live in enrichment-visualization).

GO Over-Representation Analysis

"Which biological processes are enriched in my gene list?" -> Test each GO term for over-representation of the query genes against a defined background with the one-sided hypergeometric test - because the BACKGROUND universe, not the gene list, is what decides which terms look significant.

• R: enrichGO(gene, universe, OrgDb, keyType='ENTREZID', ont='BP')

Scope: hypergeometric ORA of a gene LIST against GO terms, with background-universe selection, ID conversion, GO-DAG redundancy reduction, RNA-seq length-bias correction, and the generic enricher test for custom gene sets. A ranked-list / no-cutoff analysis -> gsea. KEGG/Reactome/WikiPathways gene sets -> kegg-pathways, reactome-pathways, wikipathways. The DE list source -> differential-expression/de-results. Plots -> enrichment-visualization.