___      .______      ______   __    __  .______
      /   \     |   _  \    /      | |  |  |  | |   _  \
     /  ^  \    |  |_)  |  |  ,----' |  |__|  | |  |_)  |
    /  /_\  \   |      /   |  |      |   __   | |      /
   /  _____  \  |  |\  \_. |  `----. |  |  |  | |  |\  \_.
  /__/     \__\ | _| `.__|  \______| |__|  |__| | _| `.__|

  https://github.com/ycl6/ArchR

Thanks for visiting this repository. If you are looking for the official ArchR package maintained by the Greenleaf Lab @ Stanford, please visit: https://github.com/GreenleafLab/ArchR

The ArchR package available here branched off from ArchR version 1.0.3 (commit 6feec35), it contains improvements and bug fixes. You can see the commit history here.

It has been tested in R version 4.5.3 and works with dependant packages from Bioconductor version 3.22.

Installation

The package is available only on GitHub, please use devtools::install_github or remotes::install_github function to install it.

For example:

# First, add Bioconductor repositories to the 'repos' option
options(repos = BiocManager::repositories())

# Use 'remotes' package to install scRUtils
remotes::install_github("ycl6/ArchR", ref="devel")

Then install other dependencies:

library(ArchR)
ArchR::installExtraPackages()

Load package

To use ArchR in a R session, load it using the library() command.

library(ArchR)

Usage

There is currently no dedicated tutorial for this version of ArchR. Please use ?somefunction or help("somefunction") to see the update-to-date documentation on the use of functions and argument list.

Useful links

• Official ArchR website: https://www.archrproject.com/
• Full manual of official ArchR: https://www.archrproject.com/bookdown
• Example 10x Multiome PBMCs analysis: https://greenleaflab.github.io/ArchR_2020/Ex-Analyze-Multiome.html
• Example Trajectory analysis: https://greenleaflab.github.io/ArchR_2020/Ex-Analyze-Trajectory.html
• Technical Report: ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis. Nat Genet 53, 403411 (2021)