RNA-seq quantifications: gene expression responses to human rhinovirus infection for 6 asthmatic and 6 non-asthmatic donors (SRP046226)
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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.