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<p><strong>Last updated:</strong> 2018-11-29</p>
<strong>workflowr checks:</strong> <small>(Click a bullet for more information)</small>
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<p><details> <summary> <strong style="color:red;">✖</strong> <strong>R Markdown file:</strong> uncommitted changes </summary> 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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<p><details> <summary> <strong style="color:blue;">✔</strong> <strong>Repository version:</strong> <a href="https://github.com/simingz/cropseq/tree/b5d096df68a9b0080889be7de234fae8926828a7" target="_blank">b5d096d</a> </summary></p>
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated. <br><br> 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:
<pre><code>
Ignored files:
Ignored: .Rproj.user/
Ignored: analysis/figure/
Untracked files:
Untracked: analysis/Quality_metrics.Rmd
Unstaged changes:
Modified: analysis/crop_workflow_Alan.Rmd
Modified: analysis/crop_workflow_Siwei.Rmd
Modified: analysis/index.Rmd
</code></pre>
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. </details>
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simingz
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2018-11-19
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<p></details></p>
<hr />
<div id="crop-seq" class="section level3">
<h3>Crop-seq</h3>
<p><a href="crop_workflow_Alan.html">Exploratory Analysis & DESeq2 from Alan</a> (11/07/2018)</p>
<p><a href="crop_workflow_Siwei.html">Exploratory Analysis from Siwei</a> (11/19/2018)</p>
<p><a href="Quality_metrics.html">Quality_metrics</a></p>
<p>In this workflow, I show how to process the raw FastQ files into count matrices representing UMI. We use the CellRanger toolkit to perform the processing. Then, we load the UMI matrices into R and perform exploratory analysis. We find that 2200+ cells have exactly 1 guide RNA and ~400 cells have zero. For the top expressed guide RNA, we perform differential expression analysis using DESeq2.</p>
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This reproducible <a href="http://rmarkdown.rstudio.com">R Markdown</a>
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