Version Compatibility

Reference examples tested with: R stats (base), ReactomePA 1.46+, clusterProfiler 4.10+

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.

Reactome Pathway Enrichment

Core Pattern - Over-Representation Analysis

Goal: Identify Reactome pathways over-represented in a gene list from differential expression or other analyses.

Approach: Test for enrichment using the hypergeometric test via ReactomePA enrichPathway against curated peer-reviewed pathways.

"Run pathway enrichment against Reactome" → Test whether genes in curated Reactome pathways are over-represented among significant genes.