ArchR is a full-featured R package for processing and analyzing single-cell ATAC-seq data. Its strength is speed and resource usage, making it possible to analyze 1 million cells in QQQ hours on a macbook pro laptop. It provides facile tools to do just about anything you would want to do with single-cell ATAC-seq data. For a more detailed description of the software, please see the publication (pdf, supplement) or the vignettes.
Please visit the ArchR website for detailed installation and usage instructions.
If you find a bug, please report it on Github. If you have questions about ArchR usage, please refer to the publication, the vignettes, or the FAQ section.