Chapter 15 Integrative Analysis with ArchR

One of the main strengths of ArchR is its ability to integrate multiple levels of information to provide novel insights. This can take the form of ATAC-seq-only analyses such as identifying peak co-accessibility to predict regulatory interactions, or analyses that integrate scRNA-seq data such as prediction of enhancer activity through peak-to-gene linkage analysis. In either case, ArchR makes it easy to garner deeper insights from your scATAC-seq data.