Day 2 learning objectives

We will use the analysis ready gene-count data generated in part 1 of the series to perform differential gene expression and functional enrichment analyses.

Set up R/RStudio

• Run RStudio on Nimbus
• Import the read-count matrix in R/RStudio

Exploratory analysis

• Learn how to perform exploratory analysis using DESeq2
• Learn how to perform principal component analysis
• Learn how to check the quality of the data and experimental design

Differential expression

• Create and understand the DESeq2 dataset object
• Identify differentially expressed genes
• Visualise differentially expressed genes

Enrichment anaylsis

• Understand and perform functional enrichement analysis using gene ontology terms
• Visualise enriched gene ontologies and pathways

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