Chapter 21 Multiomic data analysis in ArchR

This chapter provides an overview of how to analyze multiomic data in ArchR. For clarity, when we say “multiomic data”, what we are really talking about is ATAC-seq and RNA-seq acquired from the same single cells using the 10x Genomics platform. Our hope is to eventually generalize the infrastructure and workflows here to arbitrary multiomic data types and platforms but given that the vast majority of use cases focus specifically on the 10x Multiome kit, that is the first implementation we have made.

Importantly, this chapter is not meant to serve as the only thing you read if you are a new ArchR user starting with Multiome data. Instead, you should read the full manual from the start. This chapter really just shows how to work with Multiome data and load it into the ArchR ecosystem. It does not provide details on all of the other capabilities of ArchR and how to properly use them.