Differential expression analysis (Workshop on Transcriptomics 2017)

This repository provides an end-to-end tutorial of a differential expression analysis. It is a compilation of tutorials from Sean Davis and Mike Love, with additions and modifications to fit the objectives of this workshop.

Learning objectives:

• Use Salmon for gene abundance quantification.
• Import gene abundance data to R.
• Download analysis-ready datasets using recount2.
• Explore data (PCA).
• Use DESeq2 to test for differential expression using several experimental designs.
• Visualize gene expression differences.
• Explore gene lists and perform gene set enrichment analysis.