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

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<strong>Last updated:</strong> 2021-06-29
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<strong>Checks:</strong> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> 6 <span class="glyphicon glyphicon-exclamation-sign text-danger" aria-hidden="true"></span> 1
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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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<p>The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run <code>wflow_publish</code> to commit the R Markdown file and build the HTML.</p>
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The results in this page were generated with repository version <a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/tree/8cdfd4d2208ce4b2f974bbffa1cc13fed04dcd8c" target="_blank">8cdfd4d</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
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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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<pre><code>
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    Untracked:  svi-sahmri_scrna-seq-workshop_2021-july.Rproj
    Untracked:  untar_path/

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    Modified:   analysis/index.Rmd
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Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
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These are the previous versions of the repository in which changes were made to the R Markdown (<code>analysis/index.Rmd</code>) and HTML (<code>public/index.html</code>) files. If you’ve configured a remote Git repository (see <code>?wflow_git_remote</code>), click on the hyperlinks in the table below to view the files as they were in that past version.
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Rmd
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<a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/blob/8cdfd4d2208ce4b2f974bbffa1cc13fed04dcd8c/analysis/index.Rmd" target="_blank">8cdfd4d</a>
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Updating materials for workshop in July 2021
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<a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/blob/8cdfd4d2208ce4b2f974bbffa1cc13fed04dcd8c/public/index.html" target="_blank">8cdfd4d</a>
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Davis McCarthy
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2021-06-29
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Updating materials for workshop in July 2021
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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>
<p>Workshop website: [<a href="https://biocellgen-public.svi.edu.au/SVI-SAHMRI_scRNA-seq-Workshop_2021-July/public/index.html" class="uri">https://biocellgen-public.svi.edu.au/SVI-SAHMRI_scRNA-seq-Workshop_2021-July/public/index.html</a>]</p>
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<ol style="list-style-type: decimal">
<li><a href="sahmri_analysis-workflow.html">single-cell RNAseq analysis workflow for cell type identification</a></li>
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<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         
 date     2021-06-29                  

─ Packages ───────────────────────────────────────────────────────────────────
 package     * version date       lib source        
 assertthat    0.2.1   2019-03-21 [1] CRAN (R 4.0.2)
 callr         3.5.1   2020-10-13 [1] CRAN (R 4.0.2)
 cli           2.4.0   2021-04-05 [1] CRAN (R 4.0.2)
 crayon        1.4.1   2021-02-08 [1] CRAN (R 4.0.2)
 desc          1.2.0   2018-05-01 [1] CRAN (R 4.0.2)
 devtools      2.3.2   2020-09-18 [1] CRAN (R 4.0.2)
 digest        0.6.27  2020-10-24 [1] CRAN (R 4.0.2)
 ellipsis      0.3.1   2020-05-15 [1] CRAN (R 4.0.2)
 evaluate      0.14    2019-05-28 [1] CRAN (R 4.0.1)
 fansi         0.4.2   2021-01-15 [1] CRAN (R 4.0.2)
 fs            1.5.0   2020-07-31 [1] CRAN (R 4.0.2)
 git2r         0.27.1  2020-05-03 [1] CRAN (R 4.0.2)
 glue          1.4.2   2020-08-27 [1] CRAN (R 4.0.2)
 htmltools     0.5.0   2020-06-16 [1] CRAN (R 4.0.2)
 httpuv        1.5.4   2020-06-06 [1] CRAN (R 4.0.2)
 knitr         1.30    2020-09-22 [1] CRAN (R 4.0.2)
 later         1.1.0.1 2020-06-05 [1] CRAN (R 4.0.2)
 lifecycle     1.0.0   2021-02-15 [1] CRAN (R 4.0.2)
 magrittr      2.0.1   2020-11-17 [1] CRAN (R 4.0.2)
 memoise       1.1.0   2017-04-21 [1] CRAN (R 4.0.2)
 pillar        1.6.0   2021-04-13 [1] CRAN (R 4.0.2)
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 pkgload       1.1.0   2020-05-29 [1] CRAN (R 4.0.2)
 prettyunits   1.1.1   2020-01-24 [1] CRAN (R 4.0.2)
 processx      3.4.4   2020-09-03 [1] CRAN (R 4.0.2)
 promises      1.1.1   2020-06-09 [1] CRAN (R 4.0.2)
 ps            1.4.0   2020-10-07 [1] CRAN (R 4.0.2)
 R6            2.5.0   2020-10-28 [1] CRAN (R 4.0.2)
 Rcpp          1.0.5   2020-07-06 [1] CRAN (R 4.0.2)
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 stringi       1.5.3   2020-09-09 [1] CRAN (R 4.0.2)
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 testthat      3.0.0   2020-10-31 [1] CRAN (R 4.0.2)
 tibble        3.1.1   2021-04-18 [1] CRAN (R 4.0.2)
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 vctrs         0.3.7   2021-03-29 [1] CRAN (R 4.0.2)
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 whisker       0.4     2019-08-28 [1] CRAN (R 4.0.2)
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 withr         2.4.2   2021-04-18 [1] CRAN (R 4.0.2)
 workflowr     1.6.2   2020-04-30 [1] CRAN (R 4.0.2)
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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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