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<title>Analyzing regulatory chromatin in R • ArchR</title>
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<div id="archr" class="section level1">
<div class="page-header"><h1 class="hasAnchor">
<a href="#archr" class="anchor"></a>ArchR <img src="reference/figures/ArchR_dartLogo_small.jpg" alt="" width="45">
</h1></div>
<p>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 <a href="https://greenleaf.stanford.edu/assets/pdf/">publication</a> (<a href="http://greenleaf.stanford.edu/assets/pdf/">pdf</a>, <a href="http://greenleaf.stanford.edu/assets/pdf/">supplement</a>) or the <a href="articles/index.html">vignettes</a>.</p>
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<div id="installation-of-archr" class="section level1">
<h1 class="hasAnchor">
<a href="#installation-of-archr" class="anchor"></a>Installation of ArchR</h1>
<p>ArchR installation currently requires devtools. The following commands will use the Bioconductor BiocManager to install required dependences:</p>
<pre class="{r}"><code>if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
devtools::install_github("GreenleafLab/ArchR",
auth_token = token, #Need a token to download (see personalized access tokens)
repos = BiocManager::repositories()
)</code></pre>
<div id="additional-things-to-install" class="section level3">
<h3 class="hasAnchor">
<a href="#additional-things-to-install" class="anchor"></a>Additional things to install</h3>
<p>You will need a current version gfortran for mac or else you will have issues downstream. See <a href="https://github.com/fxcoudert/gfortran-for-macOS/releases" class="uri">https://github.com/fxcoudert/gfortran-for-macOS/releases</a>.</p>
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<div id="additional-packages-that-are-used-from-github" class="section level3">
<h3 class="hasAnchor">
<a href="#additional-packages-that-are-used-from-github" class="anchor"></a>Additional packages that are used from github</h3>
<p>To complete installation, you also must maually install the following packages using these devtools commands:</p>
<pre class="{r}"><code><a href="https://rdrr.io/pkg/devtools/man/remote-reexports.html"># ggrastr is a package for plotting ggplots with rastr'd points which is super helpful for large UMAPs etc
# # You need to have Cairo installed for ggrastr to work
# # On Mac OSx you need to have XQuartz (https://www.xquartz.org/)
devtools::install_github('VPetukhov/ggrastr')
# harmony is a package that can correct batch effects
devtools::install_github("immunogenomics/harmony")
# presto is a package that has efficient tools for wilcoxon tests on sparseMatrices
devtools::install_github('immunogenomics/presto')</a></code></pre>
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<div id="archr-workflow" class="section level1">
<h1 class="hasAnchor">
<a href="#archr-workflow" class="anchor"></a>ArchR Workflow</h1>
<p><img src="reference/figures/ArchR_Workflow.png" alt="" width="450"></p>
</div>
<div id="documentation" class="section level1">
<h1 class="hasAnchor">
<a href="#documentation" class="anchor"></a>Documentation</h1>
<p>Please see the navigation bar at the top of this page for links to <a href="articles/ArchR.html">a brief ArchR tutorial</a> as well as detailed <a href="articles/index.html">vignettes and examples</a> for each of the major ArchR analytical components.</p>
</div>
<div id="issues-using-archr" class="section level1">
<h1 class="hasAnchor">
<a href="#issues-using-archr" class="anchor"></a>Issues using ArchR?</h1>
<p>If you find a bug, please report it as an issue on <a href="https://github.com/GreenleafLab/ArchR/issues">Github</a>. If you think the documentation on this website or in the function annotations is unclear, please submit this as an issue on <a href="https://github.com/GreenleafLab/ArchR/issues">Github</a> with the <em>documentation</em> tag. If you have questions about ArchR usage, please refer to the <a href="https://greenleaf.stanford.edu/assets/pdf/">publication</a>, the <a href="articles/index.html">vignettes</a>, or the <a href="articles/faq.html">FAQ section</a>.</p>
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<h2>License</h2>
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<li>GPL (>= 2)</li>
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<h2>Developers</h2>
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<a href="https://twitter.com/JeffreyGranja">Jeffrey Granja</a> <br><small class="roles"> Author, maintainer </small> </li>
<li>
<a href="https://twitter.com/doctorcorces">Ryan Corces</a> <br><small class="roles"> Author </small> </li>
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<h2>Dev status</h2>
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<li><a href="https://www.tidyverse.org/lifecycle/#experimental"><img src="https://img.shields.io/badge/lifecycle-experimental-orange.svg" alt="Lifecycle: experimental"></a></li>
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<p>Developed by <a href="https://twitter.com/JeffreyGranja">Jeffrey Granja</a>, <a href="https://twitter.com/doctorcorces">Ryan Corces</a>.</p>
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