Chapter 12 Calling Peaks with ArchR

Calling peaks is one of the most fundamental processes in ATAC-seq data analysis. Because per-cell scATAC-seq data is essentially binary (accessible or not accessible), we cannot call peaks on an individual cell basis. For this reason, we defined groups of cells, typically clusters, in a previous chapter. Moreover, we created pseudo-bulk replicates to allow us to assess the reproducibility of our peak calls.