Scater: quality control of the cells

Scater: quality control of the cells

Why not use Seurat to filter outlier cells?

Seurat uses hard cutoffs to remove cells, e.g. cells with less than 200 or more than 2500 expressed genes are filtered (see Seurat tutorial). Scater is more sophisticated, it

  • provides functions for simple calculation of quality metrics
  • finds outliers using relative measures (nMADs)
  • finds outliers using combinations of quality metrics based on PCA