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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
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background-color: #f8f8f8;
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margin: 0;
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word-break: normal;
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border-radius: 3px;
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</head>
<body>
<ul>
<li><a href="#biotidy">biotidy</a>
<ul>
<li><a href="#introduction">Introduction</a></li>
<li><a href="#prepare-data">Prepare data</a></li>
<li><a href="#makepercelldf">makePerCellDF</a></li>
<li><a href="#makeperfeaturedf">makePerFeatureDF</a></li>
<li><a href="#session-information">Session information</a></li>
</ul></li>
</ul>
<!-- README.md is generated from README.Rmd. Please edit that file -->
<h1 id="biotidy">biotidy</h1>
<!-- badges: start -->
<p><a href="https://github.com/Yunuuuu/biotidy/actions/workflows/R-CMD-check.yaml"><img src="data:image/svg+xml; charset=utf-8;base64,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" alt="R-CMD-check" /></a></p>
<!-- badges: end -->
<h2 id="introduction">Introduction</h2>
<p><code>biotidy</code> package offers useful utilities for integrating
Bioinformatic objects such as SummarizedExperiment and Seurat into the
tidy(verse) framework.</p>
<p>It is important to note that <code>biotidy</code> serves a different
purpose compared to <a href="https://github.com/tidyomics">tidyomics</a>, which primarily
utilizes a pipe-based workflow for managing bioinformatic objects.
Specifically, <code>biotidy</code> provides a method for extracting a
data frame from bioinformatic objects, similar to how the
<code>broom::tidy</code> function operates on statistical model objects.
The inspiration for <code>biotidy</code> came from the functionality of
the <code>scuttle::makePerCellDF</code> and
<code>scuttle::makePerFeatureDF</code> functions on the
<code>SingleCellExperiment</code> object. The <code>biotidy</code>
package extends these functions to work with other bioinformatic
objects, such as <code>SummarizedExperiment</code>,
<code>ExpressionSet</code>, and <code>Seurat</code>.</p>
<h2 id="prepare-data">Prepare data</h2>
<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="fu">library</span>(biotidy)</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a>mocked_se <span class="ot"><-</span> <span class="fu">mockSE</span>(<span class="dv">50</span>, <span class="dv">100</span>)</span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a>mocked_sce <span class="ot"><-</span> <span class="fu">mockSCE</span>(<span class="dv">50</span>, <span class="dv">100</span>)</span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a>mocked_es <span class="ot"><-</span> <span class="fu">mockES</span>(<span class="dv">50</span>, <span class="dv">100</span>)</span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a>mocked_seurat <span class="ot"><-</span> <span class="fu">mockSeurat</span>(<span class="dv">50</span>, <span class="dv">100</span>)</span></code></pre></div>
<h2 id="makepercelldf">makePerCellDF</h2>
<p><code>makePerCellDF</code> creates a per-cell data.frame (i.e., where
each row represents a sample / cell) from the Bioinformatic objects.</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><span class="co"># SummarizedExperiment method</span></span>
<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a><span class="fu">makePerCellDF</span>(mocked_se)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>]</span>
<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a><span class="co">#> Gene0001 Gene0002 Gene0003 Gene0004 Gene0005</span></span>
<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a><span class="co">#> Cell001 119 169 7 935 0</span></span>
<span id="cb2-5"><a href="#cb2-5" tabindex="-1"></a><span class="co">#> Cell002 106 21 0 749 0</span></span>
<span id="cb2-6"><a href="#cb2-6" tabindex="-1"></a><span class="co">#> Cell003 416 52 12 1186 0</span></span>
<span id="cb2-7"><a href="#cb2-7" tabindex="-1"></a><span class="co">#> Cell004 113 24 1 586 0</span></span>
<span id="cb2-8"><a href="#cb2-8" tabindex="-1"></a><span class="co">#> Cell005 25 386 1 468 137</span></span></code></pre></div>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="fu">makePerCellDF</span>(mocked_se, <span class="at">melt =</span> <span class="cn">TRUE</span>)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>]</span>
<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a><span class="co">#> Mutation_Status Cell_Cycle Treatment .features .assay</span></span>
<span id="cb3-3"><a href="#cb3-3" tabindex="-1"></a><span class="co">#> 1 negative S treat1 Gene0001 119</span></span>
<span id="cb3-4"><a href="#cb3-4" tabindex="-1"></a><span class="co">#> 2 negative G2M treat1 Gene0001 106</span></span>
<span id="cb3-5"><a href="#cb3-5" tabindex="-1"></a><span class="co">#> 3 negative G0 treat2 Gene0001 416</span></span>
<span id="cb3-6"><a href="#cb3-6" tabindex="-1"></a><span class="co">#> 4 positive G2M treat2 Gene0001 113</span></span>
<span id="cb3-7"><a href="#cb3-7" tabindex="-1"></a><span class="co">#> 5 negative G1 treat2 Gene0001 25</span></span></code></pre></div>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="fu">makePerCellDF</span>(mocked_se, <span class="at">melt =</span> <span class="cn">TRUE</span>, <span class="at">keep_rownames =</span> <span class="cn">TRUE</span>)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>]</span>
<span id="cb4-2"><a href="#cb4-2" tabindex="-1"></a><span class="co">#> .id Mutation_Status Cell_Cycle Treatment .features</span></span>
<span id="cb4-3"><a href="#cb4-3" tabindex="-1"></a><span class="co">#> 1 Cell001 negative S treat1 Gene0001</span></span>
<span id="cb4-4"><a href="#cb4-4" tabindex="-1"></a><span class="co">#> 2 Cell002 negative G2M treat1 Gene0001</span></span>
<span id="cb4-5"><a href="#cb4-5" tabindex="-1"></a><span class="co">#> 3 Cell003 negative G0 treat2 Gene0001</span></span>
<span id="cb4-6"><a href="#cb4-6" tabindex="-1"></a><span class="co">#> 4 Cell004 positive G2M treat2 Gene0001</span></span>
<span id="cb4-7"><a href="#cb4-7" tabindex="-1"></a><span class="co">#> 5 Cell005 negative G1 treat2 Gene0001</span></span></code></pre></div>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="fu">makePerCellDF</span>(mocked_se, <span class="at">features =</span> <span class="cn">FALSE</span>, <span class="at">use_coldata =</span> <span class="cn">FALSE</span>)</span>
<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a><span class="co">#> data frame with 0 columns and 50 rows</span></span></code></pre></div>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="co"># SingleCellExperiment method</span></span>
<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="fu">makePerCellDF</span>(mocked_sce)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>]</span>
<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a><span class="co">#> Gene0001 Gene0002 Gene0003 Gene0004 Gene0005</span></span>
<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="co">#> Cell001 270 1229 0 62 206</span></span>
<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a><span class="co">#> Cell002 773 1413 1 88 216</span></span>
<span id="cb6-6"><a href="#cb6-6" tabindex="-1"></a><span class="co">#> Cell003 583 1386 0 16 432</span></span>
<span id="cb6-7"><a href="#cb6-7" tabindex="-1"></a><span class="co">#> Cell004 389 2198 0 0 13</span></span>
<span id="cb6-8"><a href="#cb6-8" tabindex="-1"></a><span class="co">#> Cell005 808 1651 0 93 21</span></span></code></pre></div>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="fu">makePerCellDF</span>(mocked_sce, <span class="at">melt =</span> <span class="cn">TRUE</span>)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>]</span>
<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a><span class="co">#> Mutation_Status Cell_Cycle Treatment .features .assay</span></span>
<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a><span class="co">#> 1 positive G1 treat1 Gene0001 270</span></span>
<span id="cb7-4"><a href="#cb7-4" tabindex="-1"></a><span class="co">#> 2 negative G2M treat2 Gene0001 773</span></span>
<span id="cb7-5"><a href="#cb7-5" tabindex="-1"></a><span class="co">#> 3 positive G2M treat2 Gene0001 583</span></span>
<span id="cb7-6"><a href="#cb7-6" tabindex="-1"></a><span class="co">#> 4 negative G2M treat1 Gene0001 389</span></span>
<span id="cb7-7"><a href="#cb7-7" tabindex="-1"></a><span class="co">#> 5 negative G2M treat1 Gene0001 808</span></span></code></pre></div>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a><span class="fu">makePerCellDF</span>(mocked_sce, <span class="at">melt =</span> <span class="cn">TRUE</span>, <span class="at">keep_rownames =</span> <span class="cn">TRUE</span>)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>]</span>
<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a><span class="co">#> .id Mutation_Status Cell_Cycle Treatment .features</span></span>
<span id="cb8-3"><a href="#cb8-3" tabindex="-1"></a><span class="co">#> 1 Cell001 positive G1 treat1 Gene0001</span></span>
<span id="cb8-4"><a href="#cb8-4" tabindex="-1"></a><span class="co">#> 2 Cell002 negative G2M treat2 Gene0001</span></span>
<span id="cb8-5"><a href="#cb8-5" tabindex="-1"></a><span class="co">#> 3 Cell003 positive G2M treat2 Gene0001</span></span>
<span id="cb8-6"><a href="#cb8-6" tabindex="-1"></a><span class="co">#> 4 Cell004 negative G2M treat1 Gene0001</span></span>
<span id="cb8-7"><a href="#cb8-7" tabindex="-1"></a><span class="co">#> 5 Cell005 negative G2M treat1 Gene0001</span></span></code></pre></div>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a><span class="fu">makePerCellDF</span>(mocked_sce, <span class="at">features =</span> <span class="cn">FALSE</span>, <span class="at">use_coldata =</span> <span class="cn">FALSE</span>)</span>
<span id="cb9-2"><a href="#cb9-2" tabindex="-1"></a><span class="co">#> data frame with 0 columns and 50 rows</span></span></code></pre></div>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" tabindex="-1"></a><span class="co"># ExpressionSet method</span></span>
<span id="cb10-2"><a href="#cb10-2" tabindex="-1"></a><span class="fu">makePerCellDF</span>(mocked_es)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>]</span>
<span id="cb10-3"><a href="#cb10-3" tabindex="-1"></a><span class="co">#> Gene0001 Gene0002 Gene0003 Gene0004 Gene0005</span></span>
<span id="cb10-4"><a href="#cb10-4" tabindex="-1"></a><span class="co">#> Cell001 213 0 1 149 20</span></span>
<span id="cb10-5"><a href="#cb10-5" tabindex="-1"></a><span class="co">#> Cell002 678 3 0 372 0</span></span>
<span id="cb10-6"><a href="#cb10-6" tabindex="-1"></a><span class="co">#> Cell003 25 12 61 728 7</span></span>
<span id="cb10-7"><a href="#cb10-7" tabindex="-1"></a><span class="co">#> Cell004 707 14 0 556 0</span></span>
<span id="cb10-8"><a href="#cb10-8" tabindex="-1"></a><span class="co">#> Cell005 469 19 0 65 23</span></span></code></pre></div>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" tabindex="-1"></a><span class="fu">makePerCellDF</span>(mocked_es, <span class="at">melt =</span> <span class="cn">TRUE</span>)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>]</span>
<span id="cb11-2"><a href="#cb11-2" tabindex="-1"></a><span class="co">#> Mutation_Status Cell_Cycle Treatment .features .assay</span></span>
<span id="cb11-3"><a href="#cb11-3" tabindex="-1"></a><span class="co">#> 1 negative S treat1 Gene0001 213</span></span>
<span id="cb11-4"><a href="#cb11-4" tabindex="-1"></a><span class="co">#> 2 positive G0 treat2 Gene0001 678</span></span>
<span id="cb11-5"><a href="#cb11-5" tabindex="-1"></a><span class="co">#> 3 negative G2M treat2 Gene0001 25</span></span>
<span id="cb11-6"><a href="#cb11-6" tabindex="-1"></a><span class="co">#> 4 negative G1 treat1 Gene0001 707</span></span>
<span id="cb11-7"><a href="#cb11-7" tabindex="-1"></a><span class="co">#> 5 positive G2M treat1 Gene0001 469</span></span></code></pre></div>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb12-1"><a href="#cb12-1" tabindex="-1"></a><span class="fu">makePerCellDF</span>(mocked_es, <span class="at">melt =</span> <span class="cn">TRUE</span>, <span class="at">keep_rownames =</span> <span class="cn">TRUE</span>)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>]</span>
<span id="cb12-2"><a href="#cb12-2" tabindex="-1"></a><span class="co">#> .id Mutation_Status Cell_Cycle Treatment .features</span></span>
<span id="cb12-3"><a href="#cb12-3" tabindex="-1"></a><span class="co">#> 1 Cell001 negative S treat1 Gene0001</span></span>
<span id="cb12-4"><a href="#cb12-4" tabindex="-1"></a><span class="co">#> 2 Cell002 positive G0 treat2 Gene0001</span></span>
<span id="cb12-5"><a href="#cb12-5" tabindex="-1"></a><span class="co">#> 3 Cell003 negative G2M treat2 Gene0001</span></span>
<span id="cb12-6"><a href="#cb12-6" tabindex="-1"></a><span class="co">#> 4 Cell004 negative G1 treat1 Gene0001</span></span>
<span id="cb12-7"><a href="#cb12-7" tabindex="-1"></a><span class="co">#> 5 Cell005 positive G2M treat1 Gene0001</span></span></code></pre></div>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1" tabindex="-1"></a><span class="fu">makePerCellDF</span>(mocked_es, <span class="at">features =</span> <span class="cn">FALSE</span>, <span class="at">use_coldata =</span> <span class="cn">FALSE</span>)</span>
<span id="cb13-2"><a href="#cb13-2" tabindex="-1"></a><span class="co">#> data frame with 0 columns and 50 rows</span></span></code></pre></div>
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb14-1"><a href="#cb14-1" tabindex="-1"></a><span class="co"># Seurat method</span></span>
<span id="cb14-2"><a href="#cb14-2" tabindex="-1"></a><span class="fu">makePerCellDF</span>(mocked_seurat, <span class="at">layer =</span> <span class="st">"counts"</span>)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>]</span>
<span id="cb14-3"><a href="#cb14-3" tabindex="-1"></a><span class="co">#> Gene0001 Gene0002 Gene0003 Gene0004 Gene0005</span></span>
<span id="cb14-4"><a href="#cb14-4" tabindex="-1"></a><span class="co">#> Cell001 0 438 0 162 201</span></span>
<span id="cb14-5"><a href="#cb14-5" tabindex="-1"></a><span class="co">#> Cell002 1 299 0 0 499</span></span>
<span id="cb14-6"><a href="#cb14-6" tabindex="-1"></a><span class="co">#> Cell003 0 325 0 55 496</span></span>
<span id="cb14-7"><a href="#cb14-7" tabindex="-1"></a><span class="co">#> Cell004 15 442 0 0 304</span></span>
<span id="cb14-8"><a href="#cb14-8" tabindex="-1"></a><span class="co">#> Cell005 3 1536 1 0 427</span></span></code></pre></div>
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb15-1"><a href="#cb15-1" tabindex="-1"></a><span class="fu">makePerCellDF</span>(mocked_seurat, <span class="at">layer =</span> <span class="st">"counts"</span>, <span class="at">melt =</span> <span class="cn">TRUE</span>)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>]</span>
<span id="cb15-2"><a href="#cb15-2" tabindex="-1"></a><span class="co">#> orig.ident nCount_RNA nFeature_RNA Mutation_Status Cell_Cycle</span></span>
<span id="cb15-3"><a href="#cb15-3" tabindex="-1"></a><span class="co">#> 1 SeuratProject 24500 76 negative S</span></span>
<span id="cb15-4"><a href="#cb15-4" tabindex="-1"></a><span class="co">#> 2 SeuratProject 18808 80 negative S</span></span>
<span id="cb15-5"><a href="#cb15-5" tabindex="-1"></a><span class="co">#> 3 SeuratProject 22796 81 negative G2M</span></span>
<span id="cb15-6"><a href="#cb15-6" tabindex="-1"></a><span class="co">#> 4 SeuratProject 21535 74 positive S</span></span>
<span id="cb15-7"><a href="#cb15-7" tabindex="-1"></a><span class="co">#> 5 SeuratProject 22934 73 positive G2M</span></span></code></pre></div>
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb16-1"><a href="#cb16-1" tabindex="-1"></a><span class="fu">makePerCellDF</span>(mocked_seurat,</span>
<span id="cb16-2"><a href="#cb16-2" tabindex="-1"></a> <span class="at">layer =</span> <span class="st">"counts"</span>, <span class="at">melt =</span> <span class="cn">TRUE</span>, <span class="at">keep_rownames =</span> <span class="cn">TRUE</span></span>
<span id="cb16-3"><a href="#cb16-3" tabindex="-1"></a>)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>]</span>
<span id="cb16-4"><a href="#cb16-4" tabindex="-1"></a><span class="co">#> .id orig.ident nCount_RNA nFeature_RNA Mutation_Status</span></span>
<span id="cb16-5"><a href="#cb16-5" tabindex="-1"></a><span class="co">#> 1 Cell001 SeuratProject 24500 76 negative</span></span>
<span id="cb16-6"><a href="#cb16-6" tabindex="-1"></a><span class="co">#> 2 Cell002 SeuratProject 18808 80 negative</span></span>
<span id="cb16-7"><a href="#cb16-7" tabindex="-1"></a><span class="co">#> 3 Cell003 SeuratProject 22796 81 negative</span></span>
<span id="cb16-8"><a href="#cb16-8" tabindex="-1"></a><span class="co">#> 4 Cell004 SeuratProject 21535 74 positive</span></span>
<span id="cb16-9"><a href="#cb16-9" tabindex="-1"></a><span class="co">#> 5 Cell005 SeuratProject 22934 73 positive</span></span></code></pre></div>
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb17-1"><a href="#cb17-1" tabindex="-1"></a><span class="fu">makePerCellDF</span>(mocked_seurat,</span>
<span id="cb17-2"><a href="#cb17-2" tabindex="-1"></a> <span class="at">layer =</span> <span class="st">"counts"</span>, <span class="at">features =</span> <span class="cn">FALSE</span>,</span>
<span id="cb17-3"><a href="#cb17-3" tabindex="-1"></a> <span class="at">use_coldata =</span> <span class="cn">FALSE</span></span>
<span id="cb17-4"><a href="#cb17-4" tabindex="-1"></a>)</span>
<span id="cb17-5"><a href="#cb17-5" tabindex="-1"></a><span class="co">#> data frame with 0 columns and 50 rows</span></span></code></pre></div>
<h2 id="makeperfeaturedf">makePerFeatureDF</h2>
<p><code>makePerFeatureDF</code> Create a per-feature data.frame (i.e.,
where each row represents a feature / gene).</p>
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb18-1"><a href="#cb18-1" tabindex="-1"></a><span class="co"># SummarizedExperiment method</span></span>
<span id="cb18-2"><a href="#cb18-2" tabindex="-1"></a><span class="fu">makePerFeatureDF</span>(mocked_se)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>]</span>
<span id="cb18-3"><a href="#cb18-3" tabindex="-1"></a><span class="co">#> Cell001 Cell002 Cell003 Cell004 Cell005</span></span>
<span id="cb18-4"><a href="#cb18-4" tabindex="-1"></a><span class="co">#> Gene0001 119 106 416 113 25</span></span>
<span id="cb18-5"><a href="#cb18-5" tabindex="-1"></a><span class="co">#> Gene0002 169 21 52 24 386</span></span>
<span id="cb18-6"><a href="#cb18-6" tabindex="-1"></a><span class="co">#> Gene0003 7 0 12 1 1</span></span>
<span id="cb18-7"><a href="#cb18-7" tabindex="-1"></a><span class="co">#> Gene0004 935 749 1186 586 468</span></span>
<span id="cb18-8"><a href="#cb18-8" tabindex="-1"></a><span class="co">#> Gene0005 0 0 0 0 137</span></span></code></pre></div>
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb19-1"><a href="#cb19-1" tabindex="-1"></a><span class="fu">makePerFeatureDF</span>(mocked_se, <span class="at">melt =</span> <span class="cn">TRUE</span>)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, ]</span>
<span id="cb19-2"><a href="#cb19-2" tabindex="-1"></a><span class="co">#> .cells .assay</span></span>
<span id="cb19-3"><a href="#cb19-3" tabindex="-1"></a><span class="co">#> 1 Cell001 119</span></span>
<span id="cb19-4"><a href="#cb19-4" tabindex="-1"></a><span class="co">#> 2 Cell001 169</span></span>
<span id="cb19-5"><a href="#cb19-5" tabindex="-1"></a><span class="co">#> 3 Cell001 7</span></span>
<span id="cb19-6"><a href="#cb19-6" tabindex="-1"></a><span class="co">#> 4 Cell001 935</span></span>
<span id="cb19-7"><a href="#cb19-7" tabindex="-1"></a><span class="co">#> 5 Cell001 0</span></span></code></pre></div>
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb20-1"><a href="#cb20-1" tabindex="-1"></a><span class="fu">makePerFeatureDF</span>(mocked_se, <span class="at">melt =</span> <span class="cn">TRUE</span>, <span class="at">keep_rownames =</span> <span class="cn">TRUE</span>)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, ]</span>
<span id="cb20-2"><a href="#cb20-2" tabindex="-1"></a><span class="co">#> .id .cells .assay</span></span>
<span id="cb20-3"><a href="#cb20-3" tabindex="-1"></a><span class="co">#> 1 Gene0001 Cell001 119</span></span>
<span id="cb20-4"><a href="#cb20-4" tabindex="-1"></a><span class="co">#> 2 Gene0002 Cell001 169</span></span>
<span id="cb20-5"><a href="#cb20-5" tabindex="-1"></a><span class="co">#> 3 Gene0003 Cell001 7</span></span>
<span id="cb20-6"><a href="#cb20-6" tabindex="-1"></a><span class="co">#> 4 Gene0004 Cell001 935</span></span>
<span id="cb20-7"><a href="#cb20-7" tabindex="-1"></a><span class="co">#> 5 Gene0005 Cell001 0</span></span></code></pre></div>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb21-1"><a href="#cb21-1" tabindex="-1"></a><span class="fu">makePerFeatureDF</span>(mocked_se, <span class="at">features =</span> <span class="cn">FALSE</span>, <span class="at">use_rowdata =</span> <span class="cn">FALSE</span>)</span>
<span id="cb21-2"><a href="#cb21-2" tabindex="-1"></a><span class="co">#> [1] Cell001 Cell002 Cell003 Cell004 Cell005 Cell006 Cell007 Cell008 Cell009</span></span>
<span id="cb21-3"><a href="#cb21-3" tabindex="-1"></a><span class="co">#> [10] Cell010 Cell011 Cell012 Cell013 Cell014 Cell015 Cell016 Cell017 Cell018</span></span>
<span id="cb21-4"><a href="#cb21-4" tabindex="-1"></a><span class="co">#> [19] Cell019 Cell020 Cell021 Cell022 Cell023 Cell024 Cell025 Cell026 Cell027</span></span>
<span id="cb21-5"><a href="#cb21-5" tabindex="-1"></a><span class="co">#> [28] Cell028 Cell029 Cell030 Cell031 Cell032 Cell033 Cell034 Cell035 Cell036</span></span>
<span id="cb21-6"><a href="#cb21-6" tabindex="-1"></a><span class="co">#> [37] Cell037 Cell038 Cell039 Cell040 Cell041 Cell042 Cell043 Cell044 Cell045</span></span>
<span id="cb21-7"><a href="#cb21-7" tabindex="-1"></a><span class="co">#> [46] Cell046 Cell047 Cell048 Cell049 Cell050</span></span>
<span id="cb21-8"><a href="#cb21-8" tabindex="-1"></a><span class="co">#> <0 rows> (or 0-length row.names)</span></span></code></pre></div>
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb22-1"><a href="#cb22-1" tabindex="-1"></a><span class="co"># SingleCellExperiment method</span></span>
<span id="cb22-2"><a href="#cb22-2" tabindex="-1"></a><span class="fu">makePerFeatureDF</span>(mocked_sce)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>]</span>
<span id="cb22-3"><a href="#cb22-3" tabindex="-1"></a><span class="co">#> Cell001 Cell002 Cell003 Cell004 Cell005</span></span>
<span id="cb22-4"><a href="#cb22-4" tabindex="-1"></a><span class="co">#> Gene0001 270 773 583 389 808</span></span>
<span id="cb22-5"><a href="#cb22-5" tabindex="-1"></a><span class="co">#> Gene0002 1229 1413 1386 2198 1651</span></span>
<span id="cb22-6"><a href="#cb22-6" tabindex="-1"></a><span class="co">#> Gene0003 0 1 0 0 0</span></span>
<span id="cb22-7"><a href="#cb22-7" tabindex="-1"></a><span class="co">#> Gene0004 62 88 16 0 93</span></span>
<span id="cb22-8"><a href="#cb22-8" tabindex="-1"></a><span class="co">#> Gene0005 206 216 432 13 21</span></span></code></pre></div>
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb23-1"><a href="#cb23-1" tabindex="-1"></a><span class="fu">makePerFeatureDF</span>(mocked_sce, <span class="at">melt =</span> <span class="cn">TRUE</span>)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, ]</span>
<span id="cb23-2"><a href="#cb23-2" tabindex="-1"></a><span class="co">#> .cells .assay</span></span>
<span id="cb23-3"><a href="#cb23-3" tabindex="-1"></a><span class="co">#> 1 Cell001 270</span></span>
<span id="cb23-4"><a href="#cb23-4" tabindex="-1"></a><span class="co">#> 2 Cell001 1229</span></span>
<span id="cb23-5"><a href="#cb23-5" tabindex="-1"></a><span class="co">#> 3 Cell001 0</span></span>
<span id="cb23-6"><a href="#cb23-6" tabindex="-1"></a><span class="co">#> 4 Cell001 62</span></span>
<span id="cb23-7"><a href="#cb23-7" tabindex="-1"></a><span class="co">#> 5 Cell001 206</span></span></code></pre></div>
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb24-1"><a href="#cb24-1" tabindex="-1"></a><span class="fu">makePerFeatureDF</span>(mocked_sce, <span class="at">melt =</span> <span class="cn">TRUE</span>, <span class="at">keep_rownames =</span> <span class="cn">TRUE</span>)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, ]</span>
<span id="cb24-2"><a href="#cb24-2" tabindex="-1"></a><span class="co">#> .id .cells .assay</span></span>
<span id="cb24-3"><a href="#cb24-3" tabindex="-1"></a><span class="co">#> 1 Gene0001 Cell001 270</span></span>
<span id="cb24-4"><a href="#cb24-4" tabindex="-1"></a><span class="co">#> 2 Gene0002 Cell001 1229</span></span>
<span id="cb24-5"><a href="#cb24-5" tabindex="-1"></a><span class="co">#> 3 Gene0003 Cell001 0</span></span>
<span id="cb24-6"><a href="#cb24-6" tabindex="-1"></a><span class="co">#> 4 Gene0004 Cell001 62</span></span>
<span id="cb24-7"><a href="#cb24-7" tabindex="-1"></a><span class="co">#> 5 Gene0005 Cell001 206</span></span></code></pre></div>
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb25-1"><a href="#cb25-1" tabindex="-1"></a><span class="fu">makePerFeatureDF</span>(mocked_sce, <span class="at">features =</span> <span class="cn">FALSE</span>, <span class="at">use_rowdata =</span> <span class="cn">FALSE</span>)</span>
<span id="cb25-2"><a href="#cb25-2" tabindex="-1"></a><span class="co">#> [1] Cell001 Cell002 Cell003 Cell004 Cell005 Cell006 Cell007 Cell008 Cell009</span></span>
<span id="cb25-3"><a href="#cb25-3" tabindex="-1"></a><span class="co">#> [10] Cell010 Cell011 Cell012 Cell013 Cell014 Cell015 Cell016 Cell017 Cell018</span></span>
<span id="cb25-4"><a href="#cb25-4" tabindex="-1"></a><span class="co">#> [19] Cell019 Cell020 Cell021 Cell022 Cell023 Cell024 Cell025 Cell026 Cell027</span></span>
<span id="cb25-5"><a href="#cb25-5" tabindex="-1"></a><span class="co">#> [28] Cell028 Cell029 Cell030 Cell031 Cell032 Cell033 Cell034 Cell035 Cell036</span></span>
<span id="cb25-6"><a href="#cb25-6" tabindex="-1"></a><span class="co">#> [37] Cell037 Cell038 Cell039 Cell040 Cell041 Cell042 Cell043 Cell044 Cell045</span></span>
<span id="cb25-7"><a href="#cb25-7" tabindex="-1"></a><span class="co">#> [46] Cell046 Cell047 Cell048 Cell049 Cell050</span></span>
<span id="cb25-8"><a href="#cb25-8" tabindex="-1"></a><span class="co">#> <0 rows> (or 0-length row.names)</span></span></code></pre></div>
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb26-1"><a href="#cb26-1" tabindex="-1"></a><span class="co"># ExpressionSet method</span></span>
<span id="cb26-2"><a href="#cb26-2" tabindex="-1"></a><span class="fu">makePerFeatureDF</span>(mocked_es)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>]</span>
<span id="cb26-3"><a href="#cb26-3" tabindex="-1"></a><span class="co">#> Cell001 Cell002 Cell003 Cell004 Cell005</span></span>
<span id="cb26-4"><a href="#cb26-4" tabindex="-1"></a><span class="co">#> Gene0001 213 678 25 707 469</span></span>
<span id="cb26-5"><a href="#cb26-5" tabindex="-1"></a><span class="co">#> Gene0002 0 3 12 14 19</span></span>
<span id="cb26-6"><a href="#cb26-6" tabindex="-1"></a><span class="co">#> Gene0003 1 0 61 0 0</span></span>
<span id="cb26-7"><a href="#cb26-7" tabindex="-1"></a><span class="co">#> Gene0004 149 372 728 556 65</span></span>
<span id="cb26-8"><a href="#cb26-8" tabindex="-1"></a><span class="co">#> Gene0005 20 0 7 0 23</span></span></code></pre></div>
<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb27-1"><a href="#cb27-1" tabindex="-1"></a><span class="fu">makePerFeatureDF</span>(mocked_es, <span class="at">melt =</span> <span class="cn">TRUE</span>)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, ]</span>
<span id="cb27-2"><a href="#cb27-2" tabindex="-1"></a><span class="co">#> .cells .assay</span></span>
<span id="cb27-3"><a href="#cb27-3" tabindex="-1"></a><span class="co">#> 1 Cell001 213</span></span>
<span id="cb27-4"><a href="#cb27-4" tabindex="-1"></a><span class="co">#> 2 Cell001 0</span></span>
<span id="cb27-5"><a href="#cb27-5" tabindex="-1"></a><span class="co">#> 3 Cell001 1</span></span>
<span id="cb27-6"><a href="#cb27-6" tabindex="-1"></a><span class="co">#> 4 Cell001 149</span></span>
<span id="cb27-7"><a href="#cb27-7" tabindex="-1"></a><span class="co">#> 5 Cell001 20</span></span></code></pre></div>
<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb28-1"><a href="#cb28-1" tabindex="-1"></a><span class="fu">makePerFeatureDF</span>(mocked_es, <span class="at">melt =</span> <span class="cn">TRUE</span>, <span class="at">keep_rownames =</span> <span class="cn">TRUE</span>)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, ]</span>
<span id="cb28-2"><a href="#cb28-2" tabindex="-1"></a><span class="co">#> .id .cells .assay</span></span>
<span id="cb28-3"><a href="#cb28-3" tabindex="-1"></a><span class="co">#> 1 Gene0001 Cell001 213</span></span>
<span id="cb28-4"><a href="#cb28-4" tabindex="-1"></a><span class="co">#> 2 Gene0002 Cell001 0</span></span>
<span id="cb28-5"><a href="#cb28-5" tabindex="-1"></a><span class="co">#> 3 Gene0003 Cell001 1</span></span>
<span id="cb28-6"><a href="#cb28-6" tabindex="-1"></a><span class="co">#> 4 Gene0004 Cell001 149</span></span>
<span id="cb28-7"><a href="#cb28-7" tabindex="-1"></a><span class="co">#> 5 Gene0005 Cell001 20</span></span></code></pre></div>
<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb29-1"><a href="#cb29-1" tabindex="-1"></a><span class="fu">makePerFeatureDF</span>(mocked_es, <span class="at">features =</span> <span class="cn">FALSE</span>, <span class="at">use_rowdata =</span> <span class="cn">FALSE</span>)</span>
<span id="cb29-2"><a href="#cb29-2" tabindex="-1"></a><span class="co">#> [1] Cell001 Cell002 Cell003 Cell004 Cell005 Cell006 Cell007 Cell008 Cell009</span></span>
<span id="cb29-3"><a href="#cb29-3" tabindex="-1"></a><span class="co">#> [10] Cell010 Cell011 Cell012 Cell013 Cell014 Cell015 Cell016 Cell017 Cell018</span></span>
<span id="cb29-4"><a href="#cb29-4" tabindex="-1"></a><span class="co">#> [19] Cell019 Cell020 Cell021 Cell022 Cell023 Cell024 Cell025 Cell026 Cell027</span></span>
<span id="cb29-5"><a href="#cb29-5" tabindex="-1"></a><span class="co">#> [28] Cell028 Cell029 Cell030 Cell031 Cell032 Cell033 Cell034 Cell035 Cell036</span></span>
<span id="cb29-6"><a href="#cb29-6" tabindex="-1"></a><span class="co">#> [37] Cell037 Cell038 Cell039 Cell040 Cell041 Cell042 Cell043 Cell044 Cell045</span></span>
<span id="cb29-7"><a href="#cb29-7" tabindex="-1"></a><span class="co">#> [46] Cell046 Cell047 Cell048 Cell049 Cell050</span></span>
<span id="cb29-8"><a href="#cb29-8" tabindex="-1"></a><span class="co">#> <0 rows> (or 0-length row.names)</span></span></code></pre></div>
<div class="sourceCode" id="cb30"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb30-1"><a href="#cb30-1" tabindex="-1"></a><span class="co"># Seurat method</span></span>
<span id="cb30-2"><a href="#cb30-2" tabindex="-1"></a><span class="fu">makePerFeatureDF</span>(mocked_seurat, <span class="at">layer =</span> <span class="st">"counts"</span>)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>]</span>
<span id="cb30-3"><a href="#cb30-3" tabindex="-1"></a><span class="co">#> Cell001 Cell002 Cell003 Cell004 Cell005</span></span>
<span id="cb30-4"><a href="#cb30-4" tabindex="-1"></a><span class="co">#> Gene0001 0 1 0 15 3</span></span>
<span id="cb30-5"><a href="#cb30-5" tabindex="-1"></a><span class="co">#> Gene0002 438 299 325 442 1536</span></span>
<span id="cb30-6"><a href="#cb30-6" tabindex="-1"></a><span class="co">#> Gene0003 0 0 0 0 1</span></span>
<span id="cb30-7"><a href="#cb30-7" tabindex="-1"></a><span class="co">#> Gene0004 162 0 55 0 0</span></span>
<span id="cb30-8"><a href="#cb30-8" tabindex="-1"></a><span class="co">#> Gene0005 201 499 496 304 427</span></span></code></pre></div>
<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb31-1"><a href="#cb31-1" tabindex="-1"></a><span class="fu">makePerFeatureDF</span>(mocked_seurat, <span class="at">layer =</span> <span class="st">"counts"</span>, <span class="at">melt =</span> <span class="cn">TRUE</span>)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, ]</span>
<span id="cb31-2"><a href="#cb31-2" tabindex="-1"></a><span class="co">#> .cells .assay</span></span>
<span id="cb31-3"><a href="#cb31-3" tabindex="-1"></a><span class="co">#> 1 Cell001 0</span></span>
<span id="cb31-4"><a href="#cb31-4" tabindex="-1"></a><span class="co">#> 2 Cell001 438</span></span>
<span id="cb31-5"><a href="#cb31-5" tabindex="-1"></a><span class="co">#> 3 Cell001 0</span></span>
<span id="cb31-6"><a href="#cb31-6" tabindex="-1"></a><span class="co">#> 4 Cell001 162</span></span>
<span id="cb31-7"><a href="#cb31-7" tabindex="-1"></a><span class="co">#> 5 Cell001 201</span></span></code></pre></div>
<div class="sourceCode" id="cb32"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb32-1"><a href="#cb32-1" tabindex="-1"></a><span class="fu">makePerFeatureDF</span>(mocked_seurat,</span>
<span id="cb32-2"><a href="#cb32-2" tabindex="-1"></a> <span class="at">layer =</span> <span class="st">"counts"</span>, <span class="at">melt =</span> <span class="cn">TRUE</span>, <span class="at">keep_rownames =</span> <span class="cn">TRUE</span></span>
<span id="cb32-3"><a href="#cb32-3" tabindex="-1"></a>)[<span class="dv">1</span><span class="sc">:</span><span class="dv">5</span>, ]</span>
<span id="cb32-4"><a href="#cb32-4" tabindex="-1"></a><span class="co">#> .id .cells .assay</span></span>
<span id="cb32-5"><a href="#cb32-5" tabindex="-1"></a><span class="co">#> 1 Gene0001 Cell001 0</span></span>
<span id="cb32-6"><a href="#cb32-6" tabindex="-1"></a><span class="co">#> 2 Gene0002 Cell001 438</span></span>
<span id="cb32-7"><a href="#cb32-7" tabindex="-1"></a><span class="co">#> 3 Gene0003 Cell001 0</span></span>
<span id="cb32-8"><a href="#cb32-8" tabindex="-1"></a><span class="co">#> 4 Gene0004 Cell001 162</span></span>
<span id="cb32-9"><a href="#cb32-9" tabindex="-1"></a><span class="co">#> 5 Gene0005 Cell001 201</span></span></code></pre></div>
<div class="sourceCode" id="cb33"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb33-1"><a href="#cb33-1" tabindex="-1"></a><span class="fu">makePerFeatureDF</span>(mocked_seurat,</span>
<span id="cb33-2"><a href="#cb33-2" tabindex="-1"></a> <span class="at">layer =</span> <span class="st">"counts"</span>, <span class="at">features =</span> <span class="cn">FALSE</span>,</span>
<span id="cb33-3"><a href="#cb33-3" tabindex="-1"></a> <span class="at">use_rowdata =</span> <span class="cn">FALSE</span></span>
<span id="cb33-4"><a href="#cb33-4" tabindex="-1"></a>)</span>
<span id="cb33-5"><a href="#cb33-5" tabindex="-1"></a><span class="co">#> [1] Cell001 Cell002 Cell003 Cell004 Cell005 Cell006 Cell007 Cell008 Cell009</span></span>
<span id="cb33-6"><a href="#cb33-6" tabindex="-1"></a><span class="co">#> [10] Cell010 Cell011 Cell012 Cell013 Cell014 Cell015 Cell016 Cell017 Cell018</span></span>
<span id="cb33-7"><a href="#cb33-7" tabindex="-1"></a><span class="co">#> [19] Cell019 Cell020 Cell021 Cell022 Cell023 Cell024 Cell025 Cell026 Cell027</span></span>
<span id="cb33-8"><a href="#cb33-8" tabindex="-1"></a><span class="co">#> [28] Cell028 Cell029 Cell030 Cell031 Cell032 Cell033 Cell034 Cell035 Cell036</span></span>
<span id="cb33-9"><a href="#cb33-9" tabindex="-1"></a><span class="co">#> [37] Cell037 Cell038 Cell039 Cell040 Cell041 Cell042 Cell043 Cell044 Cell045</span></span>
<span id="cb33-10"><a href="#cb33-10" tabindex="-1"></a><span class="co">#> [46] Cell046 Cell047 Cell048 Cell049 Cell050</span></span>
<span id="cb33-11"><a href="#cb33-11" tabindex="-1"></a><span class="co">#> <0 rows> (or 0-length row.names)</span></span></code></pre></div>
<h2 id="session-information">Session information</h2>
<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb34-1"><a href="#cb34-1" tabindex="-1"></a><span class="fu">sessionInfo</span>()</span>
<span id="cb34-2"><a href="#cb34-2" tabindex="-1"></a><span class="co">#> R version 4.4.0 (2024-04-24)</span></span>
<span id="cb34-3"><a href="#cb34-3" tabindex="-1"></a><span class="co">#> Platform: x86_64-pc-linux-gnu</span></span>
<span id="cb34-4"><a href="#cb34-4" tabindex="-1"></a><span class="co">#> Running under: Ubuntu 24.04 LTS</span></span>
<span id="cb34-5"><a href="#cb34-5" tabindex="-1"></a><span class="co">#> </span></span>
<span id="cb34-6"><a href="#cb34-6" tabindex="-1"></a><span class="co">#> Matrix products: default</span></span>
<span id="cb34-7"><a href="#cb34-7" tabindex="-1"></a><span class="co">#> BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libmkl_rt.so; LAPACK version 3.8.0</span></span>
<span id="cb34-8"><a href="#cb34-8" tabindex="-1"></a><span class="co">#> </span></span>
<span id="cb34-9"><a href="#cb34-9" tabindex="-1"></a><span class="co">#> locale:</span></span>
<span id="cb34-10"><a href="#cb34-10" tabindex="-1"></a><span class="co">#> [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 </span></span>
<span id="cb34-11"><a href="#cb34-11" tabindex="-1"></a><span class="co">#> [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 </span></span>
<span id="cb34-12"><a href="#cb34-12" tabindex="-1"></a><span class="co">#> [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C </span></span>
<span id="cb34-13"><a href="#cb34-13" tabindex="-1"></a><span class="co">#> [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C </span></span>
<span id="cb34-14"><a href="#cb34-14" tabindex="-1"></a><span class="co">#> </span></span>
<span id="cb34-15"><a href="#cb34-15" tabindex="-1"></a><span class="co">#> time zone: Asia/Shanghai</span></span>
<span id="cb34-16"><a href="#cb34-16" tabindex="-1"></a><span class="co">#> tzcode source: system (glibc)</span></span>
<span id="cb34-17"><a href="#cb34-17" tabindex="-1"></a><span class="co">#> </span></span>
<span id="cb34-18"><a href="#cb34-18" tabindex="-1"></a><span class="co">#> attached base packages:</span></span>
<span id="cb34-19"><a href="#cb34-19" tabindex="-1"></a><span class="co">#> [1] stats graphics grDevices utils datasets methods base </span></span>
<span id="cb34-20"><a href="#cb34-20" tabindex="-1"></a><span class="co">#> </span></span>
<span id="cb34-21"><a href="#cb34-21" tabindex="-1"></a><span class="co">#> other attached packages:</span></span>
<span id="cb34-22"><a href="#cb34-22" tabindex="-1"></a><span class="co">#> [1] biotidy_0.99.0</span></span>
<span id="cb34-23"><a href="#cb34-23" tabindex="-1"></a><span class="co">#> </span></span>
<span id="cb34-24"><a href="#cb34-24" tabindex="-1"></a><span class="co">#> loaded via a namespace (and not attached):</span></span>
<span id="cb34-25"><a href="#cb34-25" tabindex="-1"></a><span class="co">#> [1] Matrix_1.7-0 future.apply_1.11.2 </span></span>
<span id="cb34-26"><a href="#cb34-26" tabindex="-1"></a><span class="co">#> [3] jsonlite_1.8.8 compiler_4.4.0 </span></span>
<span id="cb34-27"><a href="#cb34-27" tabindex="-1"></a><span class="co">#> [5] crayon_1.5.3 Rcpp_1.0.12 </span></span>
<span id="cb34-28"><a href="#cb34-28" tabindex="-1"></a><span class="co">#> [7] SeuratObject_5.0.2 SummarizedExperiment_1.34.0</span></span>
<span id="cb34-29"><a href="#cb34-29" tabindex="-1"></a><span class="co">#> [9] Biobase_2.64.0 GenomicRanges_1.56.1 </span></span>
<span id="cb34-30"><a href="#cb34-30" tabindex="-1"></a><span class="co">#> [11] parallel_4.4.0 globals_0.16.3 </span></span>
<span id="cb34-31"><a href="#cb34-31" tabindex="-1"></a><span class="co">#> [13] IRanges_2.38.0 yaml_2.3.8 </span></span>
<span id="cb34-32"><a href="#cb34-32" tabindex="-1"></a><span class="co">#> [15] fastmap_1.2.0 lattice_0.22-6 </span></span>
<span id="cb34-33"><a href="#cb34-33" tabindex="-1"></a><span class="co">#> [17] R6_2.5.1 XVector_0.44.0 </span></span>
<span id="cb34-34"><a href="#cb34-34" tabindex="-1"></a><span class="co">#> [19] generics_0.1.3 S4Arrays_1.4.1 </span></span>
<span id="cb34-35"><a href="#cb34-35" tabindex="-1"></a><span class="co">#> [21] GenomeInfoDb_1.40.1 knitr_1.47 </span></span>
<span id="cb34-36"><a href="#cb34-36" tabindex="-1"></a><span class="co">#> [23] BiocGenerics_0.50.0 dotCall64_1.1-1 </span></span>
<span id="cb34-37"><a href="#cb34-37" tabindex="-1"></a><span class="co">#> [25] future_1.33.2 DelayedArray_0.30.1 </span></span>
<span id="cb34-38"><a href="#cb34-38" tabindex="-1"></a><span class="co">#> [27] MatrixGenerics_1.16.0 GenomeInfoDbData_1.2.12 </span></span>
<span id="cb34-39"><a href="#cb34-39" tabindex="-1"></a><span class="co">#> [29] rlang_1.1.4 sp_2.1-4 </span></span>
<span id="cb34-40"><a href="#cb34-40" tabindex="-1"></a><span class="co">#> [31] xfun_0.45 SparseArray_1.4.8 </span></span>
<span id="cb34-41"><a href="#cb34-41" tabindex="-1"></a><span class="co">#> [33] cli_3.6.3 progressr_0.14.0 </span></span>
<span id="cb34-42"><a href="#cb34-42" tabindex="-1"></a><span class="co">#> [35] zlibbioc_1.50.0 digest_0.6.36 </span></span>
<span id="cb34-43"><a href="#cb34-43" tabindex="-1"></a><span class="co">#> [37] grid_4.4.0 spam_2.10-0 </span></span>
<span id="cb34-44"><a href="#cb34-44" tabindex="-1"></a><span class="co">#> [39] lifecycle_1.0.4 S4Vectors_0.42.0 </span></span>
<span id="cb34-45"><a href="#cb34-45" tabindex="-1"></a><span class="co">#> [41] SingleCellExperiment_1.26.0 data.table_1.15.4 </span></span>
<span id="cb34-46"><a href="#cb34-46" tabindex="-1"></a><span class="co">#> [43] evaluate_0.24.0 listenv_0.9.1 </span></span>
<span id="cb34-47"><a href="#cb34-47" tabindex="-1"></a><span class="co">#> [45] codetools_0.2-20 abind_1.4-5 </span></span>
<span id="cb34-48"><a href="#cb34-48" tabindex="-1"></a><span class="co">#> [47] stats4_4.4.0 parallelly_1.37.1 </span></span>
<span id="cb34-49"><a href="#cb34-49" tabindex="-1"></a><span class="co">#> [49] rmarkdown_2.27 httr_1.4.7 </span></span>
<span id="cb34-50"><a href="#cb34-50" tabindex="-1"></a><span class="co">#> [51] matrixStats_1.3.0 tools_4.4.0 </span></span>
<span id="cb34-51"><a href="#cb34-51" tabindex="-1"></a><span class="co">#> [53] htmltools_0.5.8.1 UCSC.utils_1.0.0</span></span></code></pre></div>
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