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