Version Compatibility

Reference examples tested with: DESeq2 1.42+, edgeR 4.0+, ggplot2 3.5+, limma 3.58+, matplotlib 3.8+

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.

DE Visualization

Create visualizations for differential expression analysis using DESeq2 and edgeR built-in plotting functions.

Scope