ArchR is a full-featured R package for processing and analyzing single-cell ATAC-seq data. ArchR provides the most extensive suite of scATAC-seq analysis tools of any software available. Additionally, ArchR excels in both speed and resource usage, making it possible to analyze 1 million cells in 8 hours on a MacBook Pro laptop.
To get started, we recommend running through the brief ArchR tutorial. For a detailed description of all of the features of ArchR applied to a test dataset of hematopoietic cells, please see the searchable full manual. If you havent already done so, we also recommend reading the publication to get a better idea of what ArchR can do.
If you find a bug, please report it as an issue on Github. If you think the documentation on this website or in the function annotations is unclear, please submit this as an issue on Github with the documentation tag. If you have questions about ArchR usage, please refer to the the searchable full user's manual, the FAQ section, and the publication. If none of these options help, send us an email. We will do our best to respond to questions that are not otherwise answered in the documentation.