Week 14: RNA-Seq count data analysis in R
1 Overview
This is the final lecture of the R program. This week, we will cover the use of the DESeq2 package to identify differentially expressed genes (both up-regulated and down-regulated). We will begin by learning how to create a DESeq2 object, which consists of three key components: metadata, count table, and statistical design. After that, we will perform differential expression analysis and visualize the results using a volcano plot.
2 Lectures & Learning goals
Some of the things you will learn this week:
RNA-Seq count data analysis in R
- Create an R object that also incorporates the metadata
- Perform exploratory data analysis including a PCA
- Run a Differential Expression (DE) analysis
- Extract and visualize the DE results
3 Assignments and exercises
- Final Project progress report (Due 12/01)
- Exercises for this week