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README.html
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<body>
<h1 id="single-cell-analysis-of-host-microbiome-interactions">Single-cell
Analysis of Host-Microbiome Interactions</h1>
<!-- README.md is generated from README.Rmd. Please edit that file -->
<!-- badges: start -->
<!-- badges: end -->
<h2 id="installation">Installation</h2>
<p>Here, we use <code>pak</code> to install package, you can also use
<code>remotes</code></p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span><span class="fu">requireNamespace</span>(<span class="st">"pak"</span>)) {</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"pak"</span>,</span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a> <span class="at">repos =</span> <span class="fu">sprintf</span>(</span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a> <span class="st">"https://r-lib.github.io/p/pak/devel/%s/%s/%s"</span>,</span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a> .Platform<span class="sc">$</span>pkgType, <span class="fu">R.Version</span>()<span class="sc">$</span>os, <span class="fu">R.Version</span>()<span class="sc">$</span>arch</span>
<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a> )</span>
<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a> )</span>
<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a>}</span></code></pre></div>
<p><code>rsami</code> depends on <a href="https://rpolars.github.io/index.html">polars</a>, you can install
it by:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a>pak<span class="sc">::</span><span class="fu">repo_add</span>(<span class="st">"https://rpolars.r-universe.dev"</span>)</span>
<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a>pak<span class="sc">::</span><span class="fu">pkg_install</span>(<span class="st">"polars"</span>)</span></code></pre></div>
<p>You can also install the development version of <code>polars</code>
from <a href="https://github.com/pola-rs/r-polars">Github</a></p>
<p>In this way, you must install <code>rustc</code> to compile
<code>polars</code></p>
<p>You can install <code>rustc</code> with <code>rustup</code>:</p>
<pre><code>curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh</code></pre>
<p>Then install the <code>polars</code> package:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a>pak<span class="sc">::</span><span class="fu">pkg_install</span>(<span class="st">"pola-rs/r-polars"</span>)</span></code></pre></div>
<p>You can install the development version of <code>rsahmi</code> from
<a href="https://github.com/Yunuuuu/rsahmi">GitHub</a>:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a>pak<span class="sc">::</span><span class="fu">pkg_install</span>(<span class="st">"Yunuuuu/rsahmi"</span>)</span></code></pre></div>
<p>You must also install <a href="https://bioinf.shenwei.me/seqkit/">seqkit</a> and <a href="https://github.com/DerrickWood/kraken2/wiki/Manual">kraken2</a>.</p>
<h2 id="cite">Cite</h2>
<p>If you use this package, please cite:</p>
<ul>
<li>Ghaddar B, Biswas A, Harris C, Omary MB, Carpizo DR, Blaser MJ, De
S. Tumor microbiome links cellular programs and immunity in pancreatic
cancer. Cancer Cell. 2022 Oct 10;40(10):1240-1253.e5. doi:
10.1016/j.ccell.2022.09.009. PMID: 36220074; PMCID: PMC9556978.</li>
<li>Ghaddar B, Blaser MJ, De S. Denoising sparse microbial signals from
single-cell sequencing of mammalian host tissues. Nat Comput Sci. 2023
Sep;3(9):741-747. doi: 10.1038/s43588-023-00507-1. Epub 2023 Sep 18.
PMID: 37946872; PMCID: PMC10634611.</li>
<li>Song Y, Peng Y, Qin C, Jiang S, Lin J, Lai S, Wu J, Ding M, Du Y, Yu
L, Xu T. Antibiotic use attenuates response to immune checkpoint
blockade in urothelial carcinoma via inhibiting CD74-MIF/COPA: revealing
cross-talk between anti-bacterial immunity and anti-tumor immunity
through a tumor marker prognostic study. Int J Surg. 2024 Jul 12. doi:
10.1097/JS9.0000000000001901. Epub ahead of print. PMID: 38995167.</li>
</ul>
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