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.
- 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.