Beginner's Guide To Using The DESeq2 Package DEGSeq2

• 1 Introduction
• 2 Input data
  • 2.1 Preparing count matrices
  • 2.2 Aligning reads to a reference
  • 2.3 Counting reads in genes
  • 2.4 Experiment data
    • 2.4.1 The DESeqDataSet, column metadata, and the design formula
    • 2.4.2 Starting from SummarizedExperiment
    • 2.4.3 Starting from count tables
  • 2.5 Collapsing technical replicates
• 3 Running the DESeq2 pipeline
  • 3.1 Preparing the data object for the analysis of interest
  • 3.2 Running the pipeline
  • 3.3 Inspecting the results table
  • 3.4 Other comparisons
  • 3.5 Multiple testing
  • 3.6 Diagnostic plots
• 4 Independent filtering
  • 4.1 Adding gene names
  • 4.2 Exporting results
• 5 Working with rlog-transformed data
  • 5.1 The rlog transform
  • 5.2 Sample distances
  • 5.3 Gene clustering
• 6 Session Info