1 Getting started

1.1 Summary

This workshop will cover the basics of single cell RNAseq analysis in R using Seurat. We will run through basic preprocessing using Seurat package (based on the the Seurat preprocessing tutorial), as well as correction of batch effects with Harmony and cell annotation using SingleR.

If you are using virtual machine (VM) provided by the workshop, you don’t need to install any R packages, and can skip the setup section.

If you are using your own computer, follow Installation and Setup instructions.