Chapter 19 Handling ArchR Output

This chapter will introduce you to how to extract data out of ArchR for your own use or for analysis with other available packages. In general, our goal is for ArchR to be your go-to software of choice for single-cell ATAC-seq and multi-omic analyses so if there are features that you feel should be added, please feel free to post in our Discussions forum on GitHub under the “Feature Requests” label. Before doing so, make sure to search old issues and discussions to make sure that this hasnt already been addressed.

To start off, ArchR makes heavy use of SummarizedExperiment objects when exporting data. Many of the “get” functions in ArchR (getMarkerFeatures(),getCoAccessibility(), getPeakToGeneLinks(), etc.) return SummarizedExperiment objects. If you are not familiar with the SummarizedExperiment package, you should invest the time to familiarize yourself with it as it serves as the basis for the majority of genomics-related data types in R. You can read more about SummarizedExperiment here. There are also multiple YouTube videos that walk through the basics. If you aren’t familiar with SummarizedExperiment objects and opperations, then the remainder of this section may not be very helpful.