3.2 Why use ArchR?

There are multiple tools for single-cell ATAC-seq analysis out there so why should you use ArchR? At the time of publication, ArchR provided features and enabled analyses that other tools did not. Since publication, other tools have released similar functionalities. Nevertheless, we believe ArchR to be the most full-featured and user-friendly analysis pacakge for scATAC-seq and multi-omic data and we aim to continue to develop ArchR to maintain that.

In addition to offering a comprehensive set of analytical tools, ArchR is also faster and uses less memory than other available tools due to heavy optimization of the data structures and parallelization methods that form the basis of the ArchR software. When analyzing more than 70,000 cells, some tools require high-performance computing environments, exceeding 128 GB of available memory (OoM = out of memory). The below benchmarking plots are certainly out of date and represent our comparison at the time of publication but the general message remains the same - ArchR scales very well to large numbers of cells.

ArchR is designed to be used on a Unix-based laptop. For experiments of moderate size (fewer than 100,000 cells), ArchR is fast enough to perform ad hoc analysis and visualize results in real time, making it possible to interact with the data in a more in-depth and biologically meaningful way. Of course, for higher cell numbers or for users that prefer server-based analysis, ArchR provides fascile export of plots and projects that can be downloaded and used after generation on a server.

Currently, ArchR is not supported to run on Windows.