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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta name="generator" content="pandoc">
<meta name="author" content="Shaun Jackman" />
<meta name="dcterms.date" content="2014-11-03" />
<title>Automating Data-analysis Pipelines</title>
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<div class="reveal">
<div class="slides">
<section id="automating-data-analysis-pipelines" class="slide level2">
<h1>Automating Data-analysis Pipelines</h1>
<p>UBC <a href="http://stat545-ubc.github.io/">STAT 545A</a>/STAT 547M<br />2014-11-03<br /><a href="http://sjackman.ca">Shaun Jackman</a> <a href="http://twitter.com/sjackman">@sjackman</a><br /><a href="http://www.stat.ubc.ca/~jenny/">Jenny Bryan</a> <a href="https://twitter.com/JennyBryan">@JennyBryan</a><br /><a href="http://creativecommons.org/licenses/by/4.0/"><img src="images/cc-by.png" alt="Creative Commons Attribution License" /></a></p>
</section>
<section><section id="pipelines-automation-dependencies" class="titleslide slide level1"><h1>Pipelines Automation Dependencies</h1></section><section id="automation" class="slide level2">
<h1>Automation</h1>
<ul>
<li>using <a href="http://tryr.codeschool.com/">R</a></li>
<li>using the <a href="http://en.wikipedia.org/wiki/Shell_script">shell</a> and <a href="https://stat.ethz.ch/R-manual/R-devel/library/utils/html/Rscript.html">Rscript</a></li>
<li>using <a href="http://en.wikipedia.org/wiki/Make_(software)">make</a></li>
</ul>
</section><section class="slide level2">
<p><a href="http://xkcd.com/1319/"><img src="http://imgs.xkcd.com/comics/automation.png" alt="Automation" /></a></p>
<p>'Automating' comes from the roots 'auto-' meaning 'self-', and 'mating', meaning 'screwing'.</p>
</section></section>
<section><section id="pipelines" class="titleslide slide level1"><h1>Pipelines</h1></section><section id="a-pipeline" class="slide level2">
<h1>A pipeline</h1>
<p>breaks up a monolithic make-all-the-things script into discrete, manageable chunks.</p>
</section><section id="each-stage-of-the-pipeline" class="slide level2">
<h1>Each stage of the pipeline</h1>
<p>… defines its input and its outputs.<br />… does <em>not</em> modify its inputs, so it is <em>idempotent</em>.</p>
<p>Rerunning a stage of the pipeline<br />produces the same results as the previous run.</p>
</section><section id="advantage-1" class="slide level2">
<h1>Advantage #1</h1>
<p>When you modify one stage of the pipeline,<br />you don't have to rerun the entire pipeline.</p>
<p>You only rerun the downstream, dependent stages.</p>
</section><section id="advantage-2" class="slide level2">
<h1>Advantage #2</h1>
<p>Divide up work amongst a group by assigning to each person stages of the pipeline design.</p>
</section><section id="advantage-3" class="slide level2">
<h1>Advantage #3</h1>
<p>You can draw pretty pictures of your pipeline,<br />because a pipeline is a graph.</p>
</section><section class="slide level2">
<p><a href="images/pipeline.gv"><img src="images/pipeline.png" alt="01_justR" /></a><br /><a href="01_justR"><em>01_justR</em></a></p>
</section></section>
<section><section id="automation-1" class="titleslide slide level1"><h1>Automation</h1></section><section id="automate-a-pipeline" class="slide level2">
<h1>Automate a pipeline</h1>
<p>… to reproduce previous results.<br />… to recreate results deleted by fat fingers.<br />… to rerun the pipeline with updated software.<br />… to run the same pipeline on a new data set.</p>
</section><section id="tools" class="slide level2">
<h1>Tools</h1>
<ul>
<li><a href="http://tryr.codeschool.com/">R</a></li>
<li>the <a href="http://en.wikipedia.org/wiki/Shell_script">shell</a> and <a href="https://stat.ethz.ch/R-manual/R-devel/library/utils/html/Rscript.html">Rscript</a></li>
<li><a href="http://en.wikipedia.org/wiki/Make_(software)">make</a></li>
</ul>
</section><section id="r" class="slide level2">
<h1>R</h1>
<pre class="sourceCode r"><code class="sourceCode r"><span class="co">#!/usr/bin/env Rscript</span>
<span class="kw">source</span>(<span class="st">"00_downloadData.R"</span>)
<span class="kw">source</span>(<span class="st">"01_filterReorder.R"</span>)
<span class="kw">source</span>(<span class="st">"02_aggregatePlot.R"</span>)</code></pre>
<div class="fragment">
<ul>
<li>Shows in what order to run the scripts.</li>
<li>You can resume the pipeline from the middle.</li>
</ul>
</div>
</section><section id="shell-and-rscript" class="slide level2">
<h1>Shell and Rscript</h1>
<pre class="sourceCode bash"><code class="sourceCode bash"><span class="co">#!/bin/sh</span>
<span class="kw">set</span> <span class="kw">-eux</span>
<span class="kw">Rscript</span> 00_downloadData.R
<span class="kw">Rscript</span> 01_filterReorder.R
<span class="kw">Rscript</span> 02_aggregatePlot.R</code></pre>
<div class="fragment">
<p>Allows you to easily run your pipeline from the shell.</p>
</div>
<div class="fragment">
<table>
<thead>
<tr class="header">
<th style="text-align: left;">Option</th>
<th style="text-align: left;">Effect</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>set -e</code></td>
<td style="text-align: left;">Stop at the first error</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>set -u</code></td>
<td style="text-align: left;">Undefined variables are an error</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>set -x</code></td>
<td style="text-align: left;">Print each command as it is run</td>
</tr>
</tbody>
</table>
</div>
</section><section id="mix-r-scripts-with-other-tools" class="slide level2">
<h1>Mix R scripts with other tools</h1>
<pre class="sourceCode bash"><code class="sourceCode bash"><span class="co">#!/bin/sh</span>
<span class="kw">set</span> <span class="kw">-eux</span>
<span class="kw">curl</span> -L http://bit.ly/lotr_raw-tsv <span class="kw">></span>lotr_raw.tsv
<span class="kw">Rscript</span> 01_filterReorder.R
<span class="kw">Rscript</span> 02_aggregatePlot.R</code></pre>
<div class="fragment">
<p>R is a good tool, but not always the best tool for the job.</p>
<p>Not sacrilege, but the principal tenet of a polyglot.</p>
</div>
</section><section id="makefile" class="slide level2">
<h1>Makefile</h1>
<pre class="sourceCode makefile"><code class="sourceCode makefile"><span class="co">#!/usr/bin/make -f</span>
<span class="dv">lotr_raw.tsv:</span>
curl -L http://bit.ly/lotr_raw-tsv >lotr_raw.tsv
<span class="dv">lotr_clean.tsv:</span><span class="dt"> 01_filterReorder.R lotr_raw.tsv</span>
Rscript 01_filterReorder.R
<span class="dv">totalWordsByFilmRace.tsv:</span><span class="dt"> 02_aggregatePlot.R lotr_clean.tsv</span>
Rscript 02_aggregatePlot.R</code></pre>
<div class="fragment">
<p>A Makefile gives both the commands<br /><em>and their dependencies</em>.</p>
</div>
</section><section id="make-is-beautiful" class="slide level2">
<h1>Make is beautiful</h1>
<p>Tell Make how to create one type of file from another<br />and which files you want to create.</p>
<div class="fragment">
<p>Make looks at which files you have<br />and figures out how to create the files that you want.</p>
</div>
</section></section>
<section><section id="dependency-graph" class="titleslide slide level1"><h1>Dependency graph</h1></section><section id="a-pipeline-is-a-graph" class="slide level2">
<h1>A pipeline is a graph</h1>
<p>Scripts and data files are vertices of the graph.</p>
<p>Dependencies between stages are edges of the graph.</p>
</section><section class="slide level2">
<p>Both scripts and data files are shown.</p>
<p><a href="images/pipeline.gv"><img src="images/pipeline.png" alt="01_justR" /></a><br /><a href="01_justR"><em>01_justR</em></a></p>
</section><section class="slide level2">
<ul>
<li>Only dependencies between scripts are shown.</li>
<li>Data files are not shown.</li>
<li>Run the scripts in <em>topographical</em> order.</li>
</ul>
<p><a href="https://sites.google.com/site/stat540diffmethleuk/code"><img src="images/stat540diffmethleuk.png" alt="STAT 540 Differential Methylation in Leukemia" /></a><br /><em>STAT 540 Differential Methylation in Leukemia</em></p>
</section><section id="order-of-dependencies" class="slide level2">
<h1>Order of dependencies</h1>
<p>A shell script gives <em>one</em> order in which you can successfully run the pipeline.</p>
<div class="fragment">
<p>Unless the pipeline is completely linear, there are likely other such orders.</p>
</div>
</section><section class="slide level2">
<p><a href="https://sites.google.com/site/stat540diffmethleuk/code"><img src="images/stat540diffmethleuk.png" alt="STAT 540 Differential Methylation in Leukemia" /></a></p>
<p>A different order of commands may be more convenient, but without information of the dependencies, you're stuck with the given order.</p>
</section></section>
<section><section id="a-reproducible-manuscript" class="titleslide slide level1"><h1>A reproducible manuscript</h1></section><section id="one-makefile" class="slide level2">
<h1>One Makefile</h1>
<ul>
<li>Downloads the data</li>
<li>Runs the command-line programs</li>
<li>Performs the statistical analyses using <a href="http://tryr.codeschool.com/">R</a></li>
<li>and Generates the TSV tables</li>
<li>Renders the figures using <a href="http://ggplot2.org/">ggplot2</a></li>
<li>Renders the supplementary material using <a href="http://rmarkdown.rstudio.com/">RMarkdown</a></li>
<li>Renders the manuscript using <a href="http://johnmacfarlane.net/pandoc/">Pandoc</a></li>
</ul>
</section><section id="turns-this" class="slide level2">
<h1>Turns this</h1>
<figure>
<img src="images/UniqTag-md.png" alt="UniqTag Markdown" /><figcaption><a href="https://github.com/sjackman/uniqtag-paper/blob/master/UniqTag.md">UniqTag Markdown</a></figcaption>
</figure>
</section><section id="into-this" class="slide level2">
<h1>Into this</h1>
<figure>
<img src="images/UniqTag-pdf.png" alt="UniqTag PDF" /><figcaption><a href="http://biorxiv.org/content/early/2014/08/01/007583.full.pdf">UniqTag PDF</a></figcaption>
</figure>
</section></section>
<section><section id="workflow" class="titleslide slide level1"><h1>Workflow</h1></section><section class="slide level2">
<p><a href="http://kieranhealy.org/blog/archives/2014/01/23/plain-text/">Plain Text, Papers, Pandoc</a> by <a href="http://kieranhealy.org/">Kieran Healy</a></p>
<figure>
<img src="images/workflow-rmd-md.png" alt="I promise this is less insane than it appears" /><figcaption>I promise this is less insane than it appears</figcaption>
</figure>
</section><section id="markdown-for-the-manuscript" class="slide level2">
<h1>Markdown for the manuscript</h1>
<p><a href="https://help.github.com/articles/markdown-basics/">Markdown</a> is a plain-text typesetting language</p>
<pre class="sourceCode markdown"><code class="sourceCode markdown">A header
========
A list:
+ <span class="fl">This text is *italic*</span>
<span class="fl">+ This text is **bold**</span></code></pre>
<h3 id="a-header">A header</h3>
<p>A list:</p>
<ul>
<li>This text is <em>italic</em></li>
<li>This text is <strong>bold</strong></li>
</ul>
</section><section id="rmarkdown" class="slide level2">
<h1>RMarkdown</h1>
<ul>
<li><a href="http://rmarkdown.rstudio.com/">RMarkdown</a> interleaves prose with <a href="http://tryr.codeschool.com/">R</a> code
<ul>
<li>to aggregate and summarize the data</li>
<li>to generate tables</li>
<li>to render figures using <a href="http://ggplot2.org/">ggplot2</a></li>
</ul></li>
<li><a href="http://rmarkdown.rstudio.com/">RMarkdown</a> is ideal for supplementary material</li>
</ul>
</section><section id="rmarkdown-example" class="slide level2">
<h1>RMarkdown example</h1>
<pre><code>The Sum of 1 + 1
================
The sum of 1 + 1 is calculated as follows.
```{r}
1 + 1
```
</code></pre>
<p><a href="article/article.Rmd"><em>article.Rmd</em></a></p>
</section><section id="the-sum-of-1-1" class="slide level2">
<h1>The Sum of 1 + 1</h1>
<p>The sum of 1 + 1 is calculated as follows.</p>
<pre class="sourceCode r"><code class="sourceCode r"><span class="dv">1</span> +<span class="st"> </span><span class="dv">1</span></code></pre>
<pre><code>## [1] 2</code></pre>
<figure>
<img src="article/figure.png" alt="Fig. 1: A graphical view of 1 + 1" /><figcaption><em>Fig. 1</em>: A graphical view of 1 + 1</figcaption>
</figure>
</section><section class="slide level2">
<p><a href="images/article.gv"><img src="images/article.png" alt="article.gv" /></a></p>
<p>Dependencies of <a href="article/Makefile"><em>article/Makefile</em></a></p>
</section><section id="render-html" class="slide level2">
<h1>Render HTML</h1>
<pre class="sourceCode makefile"><code class="sourceCode makefile"><span class="dv">%.md:</span><span class="dt"> %.Rmd</span>
Rscript -e <span class="st">'knitr::knit("</span><span class="ch">$<</span><span class="st">", "</span><span class="ch">$@</span><span class="st">")'</span>
<span class="dv">%.html:</span><span class="dt"> %.md</span>
pandoc -s -o <span class="ch">$@</span> <span class="ch">$<</span>
<span class="dv">%.html:</span><span class="dt"> %.Rmd</span>
Rscript -e <span class="st">'rmarkdown::render("</span><span class="ch">$<</span><span class="st">")'</span>
<span class="dv">article.html:</span><span class="dt"> figure.png</span>
<span class="dv">%.png:</span><span class="dt"> %.gv</span>
dot -Tpng <span class="ch">$<</span> ><span class="ch">$@</span></code></pre>
<pre class="sourceCode bash"><code class="sourceCode bash"><span class="kw">make</span> article.html</code></pre>
<pre class="sourceCode bash"><code class="sourceCode bash"><span class="kw">dot</span> -Tpng figure.gv <span class="kw">></span>figure.png
<span class="kw">Rscript</span> -e <span class="st">'rmarkdown::render("article.Rmd")'</span></code></pre>
</section><section id="knit-markdown" class="slide level2">
<h1>Knit Markdown</h1>
<pre class="sourceCode makefile"><code class="sourceCode makefile"><span class="dv">%.md:</span><span class="dt"> %.Rmd</span>
Rscript -e <span class="st">'knitr::knit("</span><span class="ch">$<</span><span class="st">", "</span><span class="ch">$@</span><span class="st">")'</span>
<span class="dv">%.html:</span><span class="dt"> %.md</span>
pandoc -s -o <span class="ch">$@</span> <span class="ch">$<</span>
<span class="dv">%.html:</span><span class="dt"> %.Rmd</span>
Rscript -e <span class="st">'rmarkdown::render("</span><span class="ch">$<</span><span class="st">")'</span>
<span class="dv">article.html:</span><span class="dt"> figure.png</span>
<span class="dv">%.png:</span><span class="dt"> %.gv</span>
dot -Tpng <span class="ch">$<</span> ><span class="ch">$@</span></code></pre>
<pre class="sourceCode bash"><code class="sourceCode bash"><span class="kw">make</span> article.md article.html</code></pre>
<pre class="sourceCode bash"><code class="sourceCode bash"><span class="kw">Rscript</span> -e <span class="st">'knitr::knit("article.Rmd", "article.md")'</span>
<span class="kw">dot</span> -Tpng figure.gv <span class="kw">></span>figure.png
<span class="kw">pandoc</span> -s -o article.html article.md</code></pre>
</section><section id="pandoc" class="slide level2">
<h1>Pandoc</h1>
<p><a href="http://johnmacfarlane.net/pandoc/">Pandoc</a> renders attractive documents and slides<br />from plain-text typesetting formats</p>
<p>It converts between every format known (just about)</p>
<ul>
<li>Markdown</li>
<li>HTML</li>
<li>LaTeX</li>
<li>PDF</li>
<li>ODT and docx (yes, really)</li>
</ul>
</section></section>
<section><section id="evolving-a-makefile" class="titleslide slide level1"><h1>Evolving a Makefile</h1></section><section class="slide level2">
<pre class="sourceCode bash"><code class="sourceCode bash"><span class="co">#!/bin/sh</span>
<span class="kw">set</span> <span class="kw">-eux</span>
<span class="kw">dot</span> -Tpng -o figure.png figure.gv
<span class="kw">Rscript</span> -e <span class="st">'knitr::knit("article.Rmd")'</span>
<span class="kw">pandoc</span> -s -o article.html article.md</code></pre>
<p>Shell script</p>
</section><section class="slide level2">
<pre class="sourceCode makefile"><code class="sourceCode makefile"><span class="dv">all:</span>
dot -Tpng -o figure.png figure.gv
Rscript -e <span class="st">'knitr::knit("article.Rmd")'</span>
pandoc -s -o article.html article.md</code></pre>
<p>First Makefile</p>
</section><section class="slide level2">
<pre class="sourceCode makefile"><code class="sourceCode makefile"><span class="dv">all:</span><span class="dt"> article.html</span>
<span class="dv">article.html:</span>
dot -Tpng -o figure.png figure.gv
Rscript -e <span class="st">'knitr::knit("article.Rmd")'</span>
pandoc -s -o article.html article.md</code></pre>
<p>Add a rule to build <code>article.html</code></p>
</section><section class="slide level2">
<pre class="sourceCode makefile"><code class="sourceCode makefile"><span class="dv">all:</span><span class="dt"> article.html</span>
<span class="dv">article.html:</span><span class="dt"> article.Rmd</span>
dot -Tpng -o figure.png figure.gv
Rscript -e <span class="st">'knitr::knit("article.Rmd")'</span>
pandoc -s -o article.html article.md</code></pre>
<p><code>article.html</code> depends on <code>article.Rmd</code></p>
</section><section class="slide level2">
<pre class="sourceCode makefile"><code class="sourceCode makefile"><span class="dv">all:</span><span class="dt"> article.html</span>
<span class="dv">figure.png:</span><span class="dt"> figure.gv</span>
dot -Tpng -o figure.png figure.gv
<span class="dv">article.md:</span><span class="dt"> article.Rmd</span>
Rscript -e <span class="st">'knitr::knit("article.Rmd")'</span>
<span class="dv">article.html:</span><span class="dt"> article.md figure.png</span>
pandoc -s -o article.html article.md</code></pre>
<p>Split one rule into three</p>
</section><section class="slide level2">
<pre class="sourceCode makefile"><code class="sourceCode makefile"><span class="dv">all:</span><span class="dt"> article.html</span>
<span class="dv">figure.png:</span><span class="dt"> figure.gv</span>
dot -Tpng -o <span class="ch">$@</span> <span class="ch">$<</span>
<span class="dv">article.md:</span><span class="dt"> article.Rmd</span>
Rscript -e <span class="st">'knitr::knit("</span><span class="ch">$<</span><span class="st">", "</span><span class="ch">$@</span><span class="st">")'</span>
<span class="dv">article.html:</span><span class="dt"> article.md figure.png</span>
pandoc -s -o <span class="ch">$@</span> <span class="ch">$<</span></code></pre>
<p>Use the variables <code>$<</code> and <code>$@</code> for the input and output file</p>
</section><section class="slide level2">
<pre class="sourceCode makefile"><code class="sourceCode makefile"><span class="dv">all:</span><span class="dt"> article.html</span>
<span class="dv">%.png:</span><span class="dt"> %.gv</span>
dot -Tpng -o <span class="ch">$@</span> <span class="ch">$<</span>
<span class="dv">%.md:</span><span class="dt"> %.Rmd</span>
Rscript -e <span class="st">'knitr::knit("</span><span class="ch">$<</span><span class="st">", "</span><span class="ch">$@</span><span class="st">")'</span>
<span class="dv">article.html:</span><span class="dt"> article.md figure.png</span>
pandoc -s -o <span class="ch">$@</span> <span class="ch">$<</span></code></pre>
<p>Use pattern rules. The <code>%</code> matches any string</p>
</section><section class="slide level2">
<pre class="sourceCode makefile"><code class="sourceCode makefile"><span class="dv">all:</span><span class="dt"> article.html</span>
<span class="dv">%.png:</span><span class="dt"> %.gv</span>
dot -Tpng -o <span class="ch">$@</span> <span class="ch">$<</span>
<span class="dv">%.md:</span><span class="dt"> %.Rmd</span>
Rscript -e <span class="st">'knitr::knit("</span><span class="ch">$<</span><span class="st">", "</span><span class="ch">$@</span><span class="st">")'</span>
<span class="dv">%.html:</span><span class="dt"> %.md</span>
pandoc -s -o <span class="ch">$@</span> <span class="ch">$<</span>
<span class="dv">article.html:</span><span class="dt"> figure.png</span></code></pre>
<p><code>article.html</code> also depends on <code>figure.png</code></p>
</section><section class="slide level2">
<pre class="sourceCode makefile"><code class="sourceCode makefile"><span class="dv">all:</span><span class="dt"> article.html</span>
<span class="dv">clean:</span>
rm -f article.md article.html figure.png
<span class="dv">%.png:</span><span class="dt"> %.gv</span>
dot -Tpng -o <span class="ch">$@</span> <span class="ch">$<</span>
<span class="dv">%.md:</span><span class="dt"> %.Rmd</span>
Rscript -e <span class="st">'knitr::knit("</span><span class="ch">$<</span><span class="st">", "</span><span class="ch">$@</span><span class="st">")'</span>
<span class="dv">%.html:</span><span class="dt"> %.md</span>
pandoc -s -o <span class="ch">$@</span> <span class="ch">$<</span>
<span class="dv">article.html:</span><span class="dt"> figure.png</span></code></pre>
<p>Add the target named <code>clean</code></p>
</section><section class="slide level2">
<pre class="sourceCode makefile"><code class="sourceCode makefile"><span class="dv">all:</span><span class="dt"> article.html</span>
<span class="dv">clean:</span>
rm -f article.md article.html figure.png
<span class="ot">.PHONY:</span><span class="dt"> all clean</span>
<span class="ot">.DELETE_ON_ERROR:</span>
<span class="ot">.SECONDARY:</span>
<span class="dv">%.png:</span><span class="dt"> %.gv</span>
dot -Tpng -o <span class="ch">$@</span> <span class="ch">$<</span>
<span class="dv">%.md:</span><span class="dt"> %.Rmd</span>
Rscript -e <span class="st">'knitr::knit("</span><span class="ch">$<</span><span class="st">", "</span><span class="ch">$@</span><span class="st">")'</span>
<span class="dv">%.html:</span><span class="dt"> %.md</span>
pandoc -s -o <span class="ch">$@</span> <span class="ch">$<</span>
<span class="dv">article.html:</span><span class="dt"> figure.png</span></code></pre>
<p>Add <code>.PHONY</code>, <code>.DELETE_ON_ERROR</code> and <code>.SECONDARY</code></p>
</section><section class="slide level2">
<pre class="sourceCode makefile"><code class="sourceCode makefile"><span class="dv">all:</span><span class="dt"> article.html</span>
<span class="dv">clean:</span>
rm -f article.md article.html figure.png
<span class="ot">.PHONY:</span><span class="dt"> all clean</span>
<span class="ot">.DELETE_ON_ERROR:</span>
<span class="ot">.SECONDARY:</span>
<span class="co"># Render a GraphViz file</span>
<span class="dv">%.png:</span><span class="dt"> %.gv</span>
dot -Tpng -o <span class="ch">$@</span> <span class="ch">$<</span>
<span class="co"># Knit a RMarkdown document</span>
<span class="dv">%.md:</span><span class="dt"> %.Rmd</span>
Rscript -e <span class="st">'knitr::knit("</span><span class="ch">$<</span><span class="st">", "</span><span class="ch">$@</span><span class="st">")'</span>
<span class="co"># Render a Markdown document to HTML</span>
<span class="dv">%.html:</span><span class="dt"> %.md</span>
pandoc -s -o <span class="ch">$@</span> <span class="ch">$<</span>
<span class="co"># Dependencies on figures</span>
<span class="dv">article.html:</span><span class="dt"> figure.png</span></code></pre>
</section></section>
<section><section id="fin" class="titleslide slide level1"><h1>fin</h1></section><section id="links" class="slide level2">
<h1>Links</h1>
<p><a href="http://stat545-ubc.github.io/">STAT 545A</a> | <a href="http://xkcd.com/1319/">xkcd automation</a><br /><a href="http://tryr.codeschool.com/">R</a> | <a href="https://stat.ethz.ch/R-manual/R-devel/library/utils/html/Rscript.html">Rscript</a> | <a href="http://en.wikipedia.org/wiki/Shell_script">shell</a> | <a href="http://en.wikipedia.org/wiki/Make_(software)">make</a><br /><a href="https://help.github.com/articles/markdown-basics/">Markdown</a> | <a href="http://rmarkdown.rstudio.com/">RMarkdown</a> | <a href="http://johnmacfarlane.net/pandoc/">Pandoc</a> | <a href="http://ggplot2.org/">ggplot2</a><br /><a href="http://kieranhealy.org/blog/archives/2014/01/23/plain-text/">Plain Text, Papers, Pandoc</a><br /><a href="https://sites.google.com/site/stat540diffmethleuk/code">STAT 540 Differential Methylation in Leukemia</a></p>
<p><a href="http://twitter.com/sjackman">@sjackman</a> | <a href="https://github.com/sjackman">github.com/sjackman</a> | <a href="http://sjackman.ca">sjackman.ca</a></p>
</section><section id="shaun-jackman" class="slide level2">
<h1>Shaun Jackman</h1>
<p><a href="http://bcgsc.ca">Genome Sciences Centre</a>, BC Cancer Agency<br />Vancouver, Canada<br /><a href="http://twitter.com/sjackman">@sjackman</a><br /><a href="https://github.com/sjackman">github.com/sjackman</a><br /><a href="http://sjackman.ca">sjackman.ca</a></p>
<figure>
<img src="images/sjackman.jpg" />
</figure>
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