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.
For installation instructions and full documentation, visit www.ArchRProject.com.
For a full walk through of installation and frequently related issues please visit www.ArchRProject.com.
First, install devtools (for installing GitHub packages) if it isn't already installed:
if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
Then, install BiocManager (for installing bioconductor packages) if it isn't already installed:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
Then, install ArchR:
devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())
Lastly, install all of the ArchR dependencies that aren't installed by default:
library(ArchR)
ArchR::installExtraPackages()
If any of these steps fails, you should identify the offending package and troubleshoot that individual installation before proceeding. Additionally, please see the ArchR website (www.ArchRProject.com) where we have installation troubleshooting tips.
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.