Version Compatibility

Reference examples tested with: clusterProfiler 4.18+, rWikiPathways 1.26+, org.Hs.eg.db 3.18+.

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.

WikiPathways is a LIVE, monthly-updated database. enrichWP, gseWP, and gson_WP all download data.wikipathways.org/current/gmt/ at run time, so the SAME code returns DIFFERENT pathways and p-values months apart with no error. current/ is not a version. For a reproducible analysis pin a dated release with downloadPathwayArchive(date='YYYYMMDD', organism=, format='gmt') and report the date. All enrichWP/gseWP/downloadPathwayArchive calls require internet at run time.

WikiPathways Enrichment

"Which community-curated WikiPathways are enriched in my genes?" -> Test WikiPathways gene sets against a gene list (ORA) or a ranked vector (GSEA), pinning a dated GMT for reproducibility - because the live monthly database changes under identical code, and the WP GMT is Entrez-keyed so any other ID type silently overlaps nothing.

• R (ORA): enrichWP(entrez, organism='Homo sapiens', universe=all_entrez)
• R (GSEA): gseWP(named_decreasing_entrez_vector, organism='Homo sapiens')
• R (reproducible): downloadPathwayArchive(date='YYYYMMDD', organism=, format='gmt') -> read.gmt -> split term -> enricher/GSEA