Perform differential expression analysis using DESeq2 on RNA-seq raw count data. Use when you have integer count matrices with biological replicates (n≥2 per group), need log fold change shrinkage for gene ranking, or want conservative p-value estimates. Best for medium to large sample sizes (n≥4 recommended). Creates DESeqDataSet objects, performs size factor normalization, estimates dispersions, and tests for differential expression using the Wald test or likelihood ratio test.