Commit 15804b75 authored by Davis McCarthy's avatar Davis McCarthy
Browse files

Checking in edits

parent 4bcd6066
......@@ -7,7 +7,7 @@ output: html_document
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, dpi = 100, warnings = FALSE)
knitr::opts_chunk$set(echo = TRUE, dpi = 100, warning = FALSE)
```
## Introduction
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......@@ -519,7 +519,7 @@ div.tocify {
<div class="tab-content">
<div id="summary" class="tab-pane fade in active">
<p>
<strong>Last updated:</strong> 2021-06-29
<strong>Last updated:</strong> 2021-06-30
</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
......@@ -610,16 +610,16 @@ 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="#strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenpublicsvisahmriscrnaseqworkshop2021julytreeed221aff8afb80d9f55333cce93c642bd51593bdtargetblanked221afa"> <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/ed221aff8afb80d9f55333cce93c642bd51593bd" target="_blank">ed221af</a> </a>
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenpublicsvisahmriscrnaseqworkshop2021julytree4bcd6066e4fd3abded90bff112ebec5495654f7atargetblank4bcd606a"> <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/4bcd6066e4fd3abded90bff112ebec5495654f7a" target="_blank">4bcd606</a> </a>
</p>
</div>
<div id="strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenpublicsvisahmriscrnaseqworkshop2021julytreeed221aff8afb80d9f55333cce93c642bd51593bdtargetblanked221afa" class="panel-collapse collapse">
<div id="strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenpublicsvisahmriscrnaseqworkshop2021julytree4bcd6066e4fd3abded90bff112ebec5495654f7atargetblank4bcd606a" 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/ed221aff8afb80d9f55333cce93c642bd51593bd" target="_blank">ed221af</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/4bcd6066e4fd3abded90bff112ebec5495654f7a" target="_blank">4bcd606</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:
......@@ -633,6 +633,9 @@ Untracked files:
Untracked: svi-sahmri_scrna-seq-workshop_2021-july.Rproj
Untracked: untar_path/
Unstaged changes:
Modified: analysis/sahmri_analysis-workflow.Rmd
</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.
......@@ -675,6 +678,40 @@ Message
Rmd
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/blob/a63decb105d13580621d75e8e59013dcbd96999c/analysis/index.Rmd" target="_blank">a63decb</a>
</td>
<td>
Davis McCarthy
</td>
<td>
2021-06-29
</td>
<td>
Minor tweaks
</td>
</tr>
<tr>
<td>
html
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/blob/bcc60d61ccac7e987e42daf457d434a03b17a705/public/index.html" target="_blank">bcc60d6</a>
</td>
<td>
Davis McCarthy
</td>
<td>
2021-06-29
</td>
<td>
Updated html pages
</td>
</tr>
<tr>
<td>
Rmd
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/blob/ed221aff8afb80d9f55333cce93c642bd51593bd/analysis/index.Rmd" target="_blank">ed221af</a>
</td>
<td>
......@@ -748,7 +785,6 @@ Updating materials for workshop in July 2021
<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>You can access everything at the <a href="https://biocellgen-public.svi.edu.au/SVI-SAHMRI_scRNA-seq-Workshop_2021-July/public/index.html">workshop website</a>.</p>
<ol style="list-style-type: decimal">
<li><a href="sahmri_analysis-workflow.html">single-cell RNAseq analysis workflow for cell type identification</a></li>
</ol>
......@@ -770,7 +806,7 @@ Updating materials for workshop in July 2021
collate en_AU.UTF-8
ctype en_AU.UTF-8
tz Australia/Melbourne
date 2021-06-29
date 2021-06-30
─ Packages ───────────────────────────────────────────────────────────────────
package * version date lib source
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