Version Compatibility

Reference examples tested with: DESeq2 1.42+

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.

Gene Set Enrichment Analysis (GSEA)

Core Concept

GSEA uses all genes ranked by a statistic (log2FC, signed p-value) rather than a subset of significant genes. It finds gene sets where members are enriched at the top or bottom of the ranked list.

Prepare Ranked Gene List

Goal: Create a sorted named vector of gene-level statistics suitable for GSEA input.