Analysis tools and QC

Learning outcomes

After having completed this chapter you will be able to:

  • Load single cell data into R
  • Explain the basic structure of a Seurat object and extract count data and metadata
  • Calculate and visualize quality measures based on:
    • mitochondrial genes
    • ribosomal genes
    • hemoglobin genes
    • relative gene expression
  • Interpret the above quality measures per cell.
  • Perform cell filtering based on quality thresholds

Material