Chapter 11 Pseudo-bulk Replicates in ArchR

Because scATAC-seq data is essentially binary - meaning any individual locus is either accessible or not accessible - we often find ourselves in the situation where we want to perform analyses that are just not possible on a single cell. Moreover, many of the analyses we would like to perform require replicates to obtain measurements of statistical significance. In single-cell data we get around these problems by creating pseudo-bulk replicates. The term pseudo-bulk refers to a grouping of single cells where the data from each single cell is combined into a single pseudo-sample that resembles a bulk ATAC-seq experiment. ArchR makes multiple such pseudo-bulk samples for each desired cell grouping, hence the term pseudo-bulk replicates. The underlying assumption in this process is that the single cells that are being grouped together are sufficiently similar that we do not care to understand the differences between them. These cell groupings are almost always derived from individual clusters or supersets of clusters that correspond to known cell types. This chapter describes the process by which ArchR generates these pseudo-bulk replicates.