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deseq2-basics

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Performs differential expression on bulk RNA-seq count data with DESeq2's negative-binomial GLM, Wald and LRT testing, apeglm/ashr/normal LFC shrinkage, independent filtering, Cook's outlier handling, VST/rlog transforms, and design formulas including paired, batch, and interaction terms. Use when running bulk DE, choosing DESeq2 over edgeR or limma-voom, building a paired or interaction design, applying LFC shrinkage for ranking or GSEA, choosing Wald vs LRT, troubleshooting padj=NA, picking VST vs rlog, importing salmon/kallisto via tximport, or analyzing prokaryotic RNA-seq.

When to use

• running bulk DE
• choosing DESeq2 over edgeR or limma-voom
• building a paired or interaction design
• applying LFC shrinkage for ranking or GSEA
• choosing Wald vs LRT
• troubleshooting padj=NA
• picking VST vs rlog
• importing salmon/kallisto via tximport

When not to use

• analyzing prokaryotic RNA-seq

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