RNA-seq | From Counts 2 Biological Insights

Last update | June 2025

RNA-seq Analysis Crash Course

Welcome! This crash course walks you through RNA-seq data analysis in R: From raw count matrices to functional interpretation of differentially expressed genes.

Learning Objectives

1. Perform quality control of the count data.
2. Identify the R commands needed to run a differential expression analysis using DESeq2.
3. Visualize the DE results.
4. Perform functional enrichment of the DE genes.
5. Visualize functionally enriched categories.

References

Attribution | These course materials are freely adapted from a combination between the following resources:

• nf-core RNA-seq tutorial: nf-core/rnaseq tutorial
• The Carpentries Incubator guided tutorial: RNA-seq analysis with Bioconductor
• The Harvard Chan Bioinformatics Core tutorial: Differential Gene Expression Analysis (bulk RNA-seq)