4 Differential Expression Analysis

This report covers differential expression (DE) analysis of bulk RNA-seq data from Escherichia coli K-12 MG1655 using DESeq2.

We test one contrast:

• Control vs Treatment — which genes change expression in response to treatment?

⭐ Important: This script assumes you have already run 01_quality_control_ecoli.Rmd and that the dds object is available in your environment. If not, re-run the QC script first.

Setup the Environment

library(tidyverse)
library(DESeq2)
library(ggpubr)
library(plotly)
library(pheatmap)
library(RColorBrewer)
library(knitr)
library(kableExtra)
library(DT)