Module 11: RNA-seq differential expression and Enrichr

This chapter treats a gene-expression matrix as a table of many related tests. You will move from TPM to a log2 scale, compare acute HIV to uninfected controls gene by gene, correct for multiple testing, and summarize the significant genes with Enrichr. Analysis code is written with cell-by-cell natural-language prompts—see Three styles of AI-assisted programming.

In this chapter

• How RNA-seq works (includes TPM and differential expression)

• Multiple testing

• Gene-set enrichment and Enrichr

• Walkthrough prompts

• Lab prompts

• Data notes: DATA.md