Chapter 2 Doublet Inference with ArchR

One major source of trouble in single-cell data is the contribution of “doublets” to the analysis. A doublet refers to a single droplet that received a single barcoded bead and more than one nucleus. This causes the reads from more than one cell to appear as a single cell that is effectively the average of the two cells. We remove these computationally and describe this doublet removal process in depth in this chapter.