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Preparing your data. Two data files are needed for this analysis: a samples table and your count table
Install required R packages (only need to run once) - after installation, we only need to load the packages. NOTE: If using an rVDI virtual machine, the R packages are already installed
Load required R packages. Unlike installing the packages, this needs to be done every time you run the analysis
Import your data files (count table and samples table) into R
Checking for outliers and batch effects
PCA plot
Pairwise samples heatmap
Identify differentially expressed (DE) genes using DESeq2
Annotating your DE genes
Volcano plot
DE genes heatmap
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