Version Compatibility

Reference examples tested with: DESeq2 1.42+, edgeR 4.0+, limma 3.58+, ggplot2 3.5+, pheatmap 1.0+, RColorBrewer 1.1+, ggrepel 0.9+, EnhancedVolcano 1.20+, matrixStats 1.2+

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

"Make the standard DE figure panel" -> Use built-in functions or thin wrappers to produce diagnostic plots (dispersion, p-value histogram, PCA, sample distance) and result plots (MA, volcano, heatmap of top DE genes, per-gene counts), interpreted as diagnostics of the underlying model.

Scope