# 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](../part4/ai_programming_styles.md).

## In this chapter

- [How RNA-seq works](how_rnaseq_works.md) (includes TPM and differential expression)
- [Multiple testing](multiple_testing.md)
- [Gene-set enrichment and Enrichr](gene_set_enrichment.md)
- [Walkthrough prompts](Module11_walkthrough_prompts.md)
- [Lab prompts](Module11_lab_prompts.md)
- Data notes: [DATA.md](DATA.md)