1 Preliminaries

In these computer exercises you will mainly use the statistical software package R. Since we will focus on just running the code and interpretation of the results, no previous exposure to R is required. If you want to learn more about R, see our Amsterdam UMC Doctoral School course Computing in R.

The goal of this computer lab is to give you an overview of some of the steps typically applied when analyzing scRNA-seq data:

  • Quality control and filtering
  • Normalization and feature selection
  • Dimensionality reduction and visualization
  • Clustering
  • Cell annotation

1.1 Setting up R

First download the Rmd (Rmarkdown) file and open it in RStudio (Alle programma’s - R - RStudio, and ‘Ignore Update’). If you didn’t do so yet, first install the different R packages that you’ll need. In order to execute R code from within RStudio, just click the green arrow head in the chunk of