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finish up part 2
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Natalie Elphick
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@ -2562,7 +2562,7 @@ class CountdownTimer {
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<section>
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<h1 class="title">Introduction to R Data Analysis - Part 1</h1>
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<h2 class="author">Natalie Elphick</h2>
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<h3 class="date">January 22nd</h3>
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<h3 class="date">January 22nd, 2024</h3>
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</section>
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<section id="section" class="slide level2">
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@ -2593,16 +2593,15 @@ Matlab etc.)</li>
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<section id="part-1" class="slide level2">
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<h2>Part 1:</h2>
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<ol type="1">
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<li><p>What is R and why should you use it?</p></li>
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<li><p>The RStudio interface</p></li>
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<li><p>File types</p></li>
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<li><p>Error messages</p></li>
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<li><p>Variables</p></li>
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<li><p>Types & data structures</p>
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<p><em>10 min break</em></p></li>
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<li><p>Math and logic operations</p></li>
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<li><p>Functions and libraries</p></li>
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<li><p>Reading data into R</p></li>
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<li>What is R and why should you use it?</li>
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<li>The RStudio interface</li>
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<li>File types</li>
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<li>Error messages</li>
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<li>Variables</li>
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<li>Types & data structures</li>
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<li>Math and logic operations</li>
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<li>Functions and libraries</li>
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<li>Reading data into R</li>
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</ol>
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</section>
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<section>
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@ -2732,13 +2731,13 @@ and periods</li>
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one style of names</li>
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</ul>
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<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Snake case</span></span>
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<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a>dog_breeds <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"Labrador Retriever"</span>,<span class="st">"Akita"</span>, <span class="st">"Bulldog"</span>)</span>
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<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a>dog_breeds <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"Labrador Retriever"</span>, <span class="st">"Akita"</span>, <span class="st">"Bulldog"</span>)</span>
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<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a></span>
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<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a><span class="co"># Period separated</span></span>
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<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a>dog.breeds <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"Labrador Retriever"</span>,<span class="st">"Akita"</span>, <span class="st">"Bulldog"</span>)</span>
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<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a>dog.breeds <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"Labrador Retriever"</span>, <span class="st">"Akita"</span>, <span class="st">"Bulldog"</span>)</span>
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<span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a></span>
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<span id="cb3-7"><a href="#cb3-7" aria-hidden="true" tabindex="-1"></a><span class="co"># Camel case</span></span>
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<span id="cb3-8"><a href="#cb3-8" aria-hidden="true" tabindex="-1"></a>DogBreeds <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"Labrador Retriever"</span>,<span class="st">"Akita"</span>, <span class="st">"Bulldog"</span>)</span></code></pre></div>
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<span id="cb3-8"><a href="#cb3-8" aria-hidden="true" tabindex="-1"></a>DogBreeds <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"Labrador Retriever"</span>, <span class="st">"Akita"</span>, <span class="st">"Bulldog"</span>)</span></code></pre></div>
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</section>
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<section id="poll-2" class="slide level2">
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<h2>Poll 2</h2>
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@ -2821,7 +2820,7 @@ types/structures</strong> (ex. nested lists)</li>
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<section id="min-break" class="title-slide slide level1">
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<h1>10 min break</h1>
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<center>
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<div class="countdown" id="timer_0b16aa2b" data-update-every="1" tabindex="0" style="right:0;bottom:0;margin:5%;padding:50px;font-size:5em;position: relative; width: min-content;">
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<div class="countdown" id="timer_386e6f50" data-update-every="1" tabindex="0" style="right:0;bottom:0;margin:5%;padding:50px;font-size:5em;position: relative; width: min-content;">
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<div class="countdown-controls"><button class="countdown-bump-down">−</button><button class="countdown-bump-up">+</button></div>
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<code class="countdown-time"><span class="countdown-digits minutes">10</span><span class="countdown-digits colon">:</span><span class="countdown-digits seconds">00</span></code>
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</div>
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@ -2966,131 +2965,6 @@ RNA-Seq Analysis Using R</a>
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<li>Feb 1, 2024 (9:30am-12:00pm)</li>
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</ul></li>
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</ol>
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</section></section>
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<section>
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<section id="chatgpt-tips-for-r" class="title-slide slide level1">
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<h1>ChatGPT Tips for R</h1>
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</section>
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<section id="general-tips" class="slide level2">
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<h2>General Tips</h2>
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<ul>
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<li>Always confirm ChatGPT’s outputs are correct</li>
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<li>Provide as much detail as possible about the problem in the 1st
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prompt</li>
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<li>Use separate chats for separate tasks/projects</li>
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<li>Try the ‘Custom Instructions’ function that adds additional
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information to every prompt</li>
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<li>Can visit webpages (GPT 4 only), which can help get more specific
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answers</li>
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</ul>
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</section>
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<section id="code-tips" class="slide level2">
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<h2>Code Tips</h2>
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<ul>
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<li>Commented R code yields better responses in my experience</li>
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<li>Provide the code and error message in the same prompt</li>
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<li>ChatGPT can work well to convert syntax and improve your code:
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<ul>
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<li>“Turn this loop into a function : [your code]”</li>
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<li>“Is there a better way to do this : [your code]”</li>
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</ul></li>
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<li>Check out the file:
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<code>example_code/1_convert_syntax_example.R</code> for an example use
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case</li>
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</ul>
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</section></section>
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<section>
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<section id="finding-r-packages" class="title-slide slide level1">
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<h1>Finding R Packages</h1>
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</section>
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<section id="key-questions" class="slide level2">
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<h2>Key Questions</h2>
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<ul>
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<li>What assay was the package designed for?</li>
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<li>When was the last release?</li>
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<li>Is it maintained (frequent updates)?</li>
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<li>Does it work on all operating systems?</li>
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<li>Are other people using it? (citations)</li>
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<li>Do they respond to github issues?</li>
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<li>Is there a benchmarking paper?</li>
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</ul>
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</section>
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<section id="bioconductor-and-cran" class="slide level2">
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<h2>BioConductor and CRAN</h2>
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<ul>
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<li><p>Both of these have stringent requirements for packages they host
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(eg. for BioConductor they have to run on all major operating
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systems)</p></li>
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<li><p>Prefer BioConductor packages if available over CRAN</p></li>
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<li><p>Prefer CRAN packages over ones only hosted on GitHub</p></li>
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</ul>
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</section>
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<section id="start-with-the-assay" class="slide level2">
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<h2>Start with the Assay</h2>
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<ul>
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<li>Click <a href="https://www.bioconductor.org/packages/release/BiocViews.html#___Sequencing">here</a>
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to go to BioC views</li>
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<li>Pick the assay you want to analyse</li>
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<li>Pick the type of analysis you want to do</li>
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<li>Find a package that does it</li>
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<li>Find benchmarking papers to narrow the list of packages down</li>
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<li>Find the vignette on the package page and refer to the manual for
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any questions not covered by it</li>
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</ul>
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</section></section>
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<section>
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<section id="additional-resources" class="title-slide slide level1">
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<h1>Additional Resources</h1>
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</section>
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<section id="r-1" class="slide level2">
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<h2>R</h2>
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<ul>
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<li><p><a href="https://bookdown.org/yihui/rmarkdown/how-to-read-this-book.html">R
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Markdown: The Definitive Guide</a> : Excellent R markdown
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reference</p></li>
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<li><p><a href="https://r4ds.hadley.nz/">R for Data Science</a></p></li>
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<li><p><a href="https://ggplot2-book.org/">ggplot2: elegant graphics for
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data analysis</a></p></li>
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<li><p><a href="https://adv-r.hadley.nz/">Advanced R</a></p></li>
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</ul>
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</section>
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<section id="statistics" class="slide level2">
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<h2>Statistics</h2>
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<ul>
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<li><a href="https://bookdown.org/steve_midway/DAR">Data Analysis in
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R</a> : This book has more statistics details than <em>R for Data
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Science</em></li>
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<li><a href="https://bookdown.org/steve_midway/DAR/glms-generalized-linear-models.html">Generalized
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Linear Models</a><br />
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</li>
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<li><a href="https://bookdown.org/steve_midway/DAR/random-effects.html">Random
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Effects</a></li>
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</ul>
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</section>
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<section id="rna-seq-analysis" class="slide level2">
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<h2>RNA-seq Analysis</h2>
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<ul>
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<li><a href="https://rnaseq.uoregon.edu/">RNA-seqlopedia</a> :
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Everything you need to know about RNA-seq experiments</li>
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<li><a href="https://luisvalesilva.com/datasimple/rna-seq_units.html">RNA-seq
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Expression Units</a> : Blog post on understanding common units</li>
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<li><a href="https://bioconductor.org/books/3.17/OSCA.intro/index.html">Introduction
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to Single-Cell Analysis with Bioconductor</a> : Covers the basics of
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scRNA-seq analysis in R</li>
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</ul>
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</section>
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<section id="dimensional-reduction" class="slide level2">
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<h2>Dimensional Reduction</h2>
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<ul>
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<li><a href="https://uw.pressbooks.pub/appliedmultivariatestatistics/chapter/pca/">Tutorial
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on PCA</a> : PCA explained with R code examples</li>
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<li><a href="https://pair-code.github.io/understanding-umap/">Understanding
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UMAP</a> : Short explanation with great visualizations, mainly useful
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for scRNA-seq analysis</li>
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</ul>
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</section></section>
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</div>
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</div>
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10031
docs/Intro_to_R_data_analysis_part_2.html
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10031
docs/Intro_to_R_data_analysis_part_2.html
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@ -8,6 +8,7 @@
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<li><a href="https://gladstone-institutes.github.io/Bioinformatics-Workshops/Intro_to_Unix_Part_1.html">Introduction to Unix - Part 1</li>
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<li><a href="https://gladstone-institutes.github.io/Bioinformatics-Workshops/Intro_to_Unix_Part_2.html">Introduction to Unix - Part 2</li>
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<li><a href="https://gladstone-institutes.github.io/Bioinformatics-Workshops/Intro_to_R_data_analysis_part_1.html">Introduction to R Data Analysis - Part 1</li>
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<li><a href="https://gladstone-institutes.github.io/Bioinformatics-Workshops/Intro_to_R_data_analysis_part_2.html">Introduction to R Data Analysis - Part 2</li>
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</ul>
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</body>
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</html>
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