Commit 4bc91394 authored by Davis McCarthy's avatar Davis McCarthy
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Updated web pages

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name: SAHMRI scRNA-seq Workshop
name: SVI-SAHMRI scRNA-seq Workshop
output_dir: ../public
navbar:
title: SAHMRI scRNA-seq Workshop
left:
- text: "Home"
href: index.html
- text: "Workshop"
href: sahmri_analysis-workflow.html
- text: "About"
href: about.html
- text: "License"
......
......@@ -428,6 +428,9 @@ div.tocify {
<li>
<a href="index.html">Home</a>
</li>
<li>
<a href="sahmri_analysis-workflow.html">Workshop</a>
</li>
<li>
<a href="about.html">About</a>
</li>
......@@ -484,7 +487,7 @@ div.tocify {
<div class="tab-content">
<div id="summary" class="tab-pane fade in active">
<p>
<strong>Last updated:</strong> 2021-07-05
<strong>Last updated:</strong> 2021-07-07
</p>
<p>
<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
......@@ -575,16 +578,16 @@ This reproducible <a href="http://rmarkdown.rstudio.com">R Markdown</a> analysis
<div class="panel panel-default">
<div class="panel-heading">
<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenpublicsvisahmriscrnaseqworkshop2021julytreec5ce76b93ee21d6cf53dc97dde57e1494e4dc759targetblankc5ce76ba"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/tree/c5ce76b93ee21d6cf53dc97dde57e1494e4dc759" target="_blank">c5ce76b</a> </a>
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenpublicsvisahmriscrnaseqworkshop2021julytreed13d36fdc07b06702dea1a463ba9cbafa1cf769etargetblankd13d36fa"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/tree/d13d36fdc07b06702dea1a463ba9cbafa1cf769e" target="_blank">d13d36f</a> </a>
</p>
</div>
<div id="strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenpublicsvisahmriscrnaseqworkshop2021julytreec5ce76b93ee21d6cf53dc97dde57e1494e4dc759targetblankc5ce76ba" class="panel-collapse collapse">
<div id="strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenpublicsvisahmriscrnaseqworkshop2021julytreed13d36fdc07b06702dea1a463ba9cbafa1cf769etargetblankd13d36fa" class="panel-collapse collapse">
<div class="panel-body">
<p>
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
</p>
<p>
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/c5ce76b93ee21d6cf53dc97dde57e1494e4dc759" target="_blank">c5ce76b</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
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/d13d36fdc07b06702dea1a463ba9cbafa1cf769e" target="_blank">d13d36f</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
</p>
<p>
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:
......@@ -595,11 +598,13 @@ Ignored files:
Ignored: .Rproj.user/
Untracked files:
Untracked: figures/
Untracked: raw_data/
Untracked: svi-sahmri_scrna-seq-workshop_2021-july.Rproj
Untracked: untar_path/
Unstaged changes:
Modified: analysis/_site.yml
</code></pre>
<p>
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.
......@@ -642,6 +647,40 @@ Message
Rmd
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/blob/d13d36fdc07b06702dea1a463ba9cbafa1cf769e/analysis/index.Rmd" target="_blank">d13d36f</a>
</td>
<td>
Davis McCarthy
</td>
<td>
2021-07-07
</td>
<td>
Updating workshop content
</td>
</tr>
<tr>
<td>
html
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/blob/9ec263660db04249b12e8997efee8d51eb9b9050/public/index.html" target="_blank">9ec2636</a>
</td>
<td>
Davis McCarthy
</td>
<td>
2021-07-05
</td>
<td>
Substantial updates to workflow
</td>
</tr>
<tr>
<td>
Rmd
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/blob/c5ce76b93ee21d6cf53dc97dde57e1494e4dc759/analysis/index.Rmd" target="_blank">c5ce76b</a>
</td>
<td>
......@@ -816,7 +855,31 @@ Updating materials for workshop in July 2021
</div>
<div id="introduction" class="section level2">
<h2>Introduction</h2>
<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>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, marker gene detection and cell type annotation - with plenty more along the way!</p>
</div>
<div id="setup-requirements" class="section level2">
<h2>Setup requirements</h2>
<p>We use the Bioconductor single-cell ecosystem for this workshop. Thus, participants will need a recent version of R (version 4.0+) and a set of specific packages that we use.</p>
<p>The code snippet below will install the necessary packages for you in R (i.e. run the following code at the R prompt in an R or RStudio session). The first line installs the <code>BiocManager</code> package, which is the preferred package for then installing Bioconductor packages. The next (long) line then installs the necessary Bioconductor packages (and any dependencies).</p>
<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><span class="fu">install.packages</span>(<span class="st">&quot;BiocManager&quot;</span>)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>BiocManager<span class="sc">::</span><span class="fu">install</span>(<span class="fu">c</span>(<span class="st">&quot;scRNAseq&quot;</span>,</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> <span class="st">&quot;scater&quot;</span>,</span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a> <span class="st">&quot;scran&quot;</span>,</span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a> <span class="st">&quot;clustree&quot;</span>,</span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a> <span class="st">&quot;BiocSingular&quot;</span>,</span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a> <span class="st">&quot;Rtsne&quot;</span>,</span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a> <span class="st">&quot;BiocFileCache&quot;</span>,</span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a> <span class="st">&quot;DropletUtils&quot;</span>,</span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a> <span class="st">&quot;EnsDb.Hsapiens.v86&quot;</span>,</span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a> <span class="st">&quot;schex&quot;</span>,</span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a> <span class="st">&quot;celldex&quot;</span>,</span>
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a> <span class="st">&quot;SingleR&quot;</span>,</span>
<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a> <span class="st">&quot;gridExtra&quot;</span>))</span></code></pre></div>
<p>If you have trouble with the package installation, please ask a colleague for help.</p>
<p>Once you have installed the packages, you’re ready to go with the workshop. So let’s…</p>
</div>
<div id="get-crackin" class="section level2">
<h2>Get crackin’</h2>
<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>
<br>
<p>
......@@ -825,7 +888,7 @@ Updating materials for workshop in July 2021
</button>
</p>
<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>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" 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)
......@@ -836,7 +899,7 @@ Updating materials for workshop in July 2021
collate en_AU.UTF-8
ctype en_AU.UTF-8
tz Australia/Melbourne
date 2021-07-05
date 2021-07-07
─ Packages ───────────────────────────────────────────────────────────────────
package * version date lib source
......@@ -883,7 +946,7 @@ Updating materials for workshop in July 2021
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2)
stringi 1.6.2 2021-05-17 [1] CRAN (R 4.0.2)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.2)
testthat 3.0.3 2021-06-16 [1] CRAN (R 4.0.2)
testthat 3.0.4 2021-07-01 [1] CRAN (R 4.0.2)
tibble 3.1.2 2021-05-16 [1] CRAN (R 4.0.2)
usethis 2.0.1 2021-02-10 [1] CRAN (R 4.0.2)
utf8 1.2.1 2021-03-12 [1] CRAN (R 4.0.2)
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