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<h1 class="title toc-ignore">SAHMRI Single-cell RNA-seq Analysis Workshop</h1>

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<p>
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<span class="glyphicon glyphicon-list" aria-hidden="true"></span> workflowr <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span>
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<a data-toggle="tab" href="#checks"> Checks <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> </a>
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<strong>Last updated:</strong> 2021-07-05
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<strong>Checks:</strong> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> 7 <span class="glyphicon glyphicon-exclamation-sign text-danger" aria-hidden="true"></span> 0
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</p>
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<strong>Knit directory:</strong> <code>svi-sahmri_scrna-seq-workshop_2021-july/</code> <span class="glyphicon glyphicon-question-sign" aria-hidden="true" title="This is the local directory in which the code in this file was executed."> </span>
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This reproducible <a href="http://rmarkdown.rstudio.com">R Markdown</a> analysis was created with <a
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRMarkdownfilestronguptodate"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>R Markdown file:</strong> up-to-date </a>
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<p>Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.</p>
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Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use <code>wflow_publish</code> or <code>wflow_git_commit</code>). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
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<div id="introduction" class="section level2">
<h2>Introduction</h2>
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<p>In this workshop, we will introduce the data infrastructure for scRNA-seq analysis in R and practice a workflow of scRNAseq analysis; from pre-processing, quality control to dimensionality reduction and clustering. We will then demonstrate the usage of marker genes for cell type annotation and an automatic approach for matching query cells to a reference atlas with labels.</p>
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<p>Follow this link for the <a href="sahmri_analysis-workflow.html">single-cell RNA-seq analysis workflow focusing on cell type identification</a>.</p>
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<button type="button" class="btn btn-default btn-workflowr btn-workflowr-sessioninfo" data-toggle="collapse" data-target="#workflowr-sessioninfo" style="display: block;">
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<div id="workflowr-sessioninfo" class="collapse">
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>devtools<span class="sc">::</span><span class="fu">session_info</span>()</span></code></pre></div>
<pre><code>─ Session info ───────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.3 (2020-10-10)
 os       macOS Big Sur 10.16         
 system   x86_64, darwin17.0          
 ui       X11                         
 language (EN)                        
 collate  en_AU.UTF-8                 
 ctype    en_AU.UTF-8                 
 tz       Australia/Melbourne         
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 date     2021-07-05                  
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─ Packages ───────────────────────────────────────────────────────────────────
 package     * version date       lib source        
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 cli           3.0.0   2021-06-30 [1] CRAN (R 4.0.3)
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[1] /Users/dmccarthy/Library/R/4.0/library
[2] /Library/Frameworks/R.framework/Versions/4.0/Resources/library</code></pre>
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