Version Compatibility

Reference examples tested with: DESeq2 1.42+, ggplot2 3.5+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, scikit-learn 1.4+, scipy 1.12+, seaborn 0.13+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• 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.

Count Matrix QC

"Check my count matrix for outliers and batch effects" → Perform PCA, sample-sample correlation, library size assessment, and outlier detection before running differential expression.

• R: DESeq2::vst() → plotPCA(), sample distance heatmap
• Python: sklearn.decomposition.PCA, seaborn.clustermap

Quality control and exploratory analysis of count matrices before differential expression.