mirror of
https://github.com/gladstone-institutes/Bioinformatics-Workshops.git
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update for May 2025
This commit is contained in:
Natalie Elphick
parent
42b000f64a
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<head>
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<meta charset="utf-8">
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<meta name="generator" content="pandoc">
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<meta name="author" content="Natalie Elphick" />
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<meta name="author" content="Natalie Gill" />
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<title>Introduction to R Data Analysis</title>
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<meta name="apple-mobile-web-app-capable" content="yes">
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<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
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@ -2571,8 +2571,8 @@ class CountdownTimer {
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<section>
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<h1 class="title">Introduction to R Data Analysis</h1>
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<h1 class="subtitle">Part 1</h1>
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<h2 class="author">Natalie Elphick</h2>
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<h3 class="date">January 27th, 2025</h3>
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<h2 class="author">Natalie Gill</h2>
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<h3 class="date">May 5th, 2025</h3>
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</section>
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<section id="section" class="slide level2">
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@ -2583,10 +2583,8 @@ class CountdownTimer {
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</section>
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<section id="introductions" class="slide level2">
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<h2>Introductions</h2>
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<p><strong>Natalie Elphick</strong><br />
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<p><strong>Natalie Gill</strong><br />
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Bioinformatician II</p>
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<p><strong>Michela Traglia</strong><br />
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Senior Statistician</p>
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</section>
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<section id="poll-1" class="slide level2">
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<h2>Poll 1</h2>
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@ -2652,8 +2650,8 @@ the end of the workshop to continue at your own pace.</li>
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<ul>
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<li>An open source language developed for statistical computing by
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<strong>R</strong>oss Ihaka and <strong>R</strong>obert Gentleman</li>
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<li>Inspired by the <strong>S</strong> language developed at Bell labs
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in 1976 to make interactive data analysis easier</li>
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<li>Developed at Bell labs in 1976 to make interactive data analysis
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easier</li>
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<li>The first official version was released in 2000</li>
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</ul>
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</section>
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@ -2883,7 +2881,7 @@ value?</strong></p>
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<li>“1.5” - Numeric</li>
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<li>“A” - Character</li>
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<li>1L - Integer</li>
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<li>TRUE - Boolean</li>
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<li>TRUE - Boolean/Logical</li>
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</ol>
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</section>
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<section id="data-structures" class="slide level2">
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@ -2923,7 +2921,7 @@ 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_45c35f34" 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_4947b529" 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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@ -3092,7 +3090,7 @@ correct format</li>
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<section id="why-use-tidyverse-packages" class="slide level2">
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<h2>Why use Tidyverse Packages?</h2>
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<ul>
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<li>Most of the work in data analysis is getting data into the correct
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<li>Much of the work in data analysis is getting data into the correct
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format to create outputs (plots and tables)</li>
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<li>The tidyverse collection of packages simplifies this process
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<ul>
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@ -3108,6 +3106,17 @@ graphics)</li>
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<section id="end-of-part-1" class="title-slide slide level1">
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<h1>End of Part 1</h1>
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</section>
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<section id="schedule-for-part-2" class="slide level2">
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<h2>Schedule for Part 2</h2>
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<ol type="1">
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<li>Introduction to Tidyverse</li>
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<li>Filtering and reformatting data</li>
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<li>Plotting data</li>
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<li>Hands on data analysis</li>
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<li>AI tips for R</li>
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<li>Where to get help</li>
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</ol>
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</section>
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<section id="workshop-survey" class="slide level2">
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<h2>Workshop survey</h2>
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@ -3118,15 +3127,12 @@ survey</a> so we can continue to improve these workshops</li>
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</section>
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<section id="upcoming-workshops" class="slide level2">
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<h2>Upcoming Workshops</h2>
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<p><a href="https://gladstone.org/events/introduction-unix-command-line-2">Introduction
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to Unix Command Line</a><br />
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February 10-February 11, 2025 1:00-3:00pm PST</p>
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<p><a href="https://gladstone.org/events/introduction-rna-seq-analysis-8">Introduction
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to RNA-Seq Analysis</a><br />
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February 13-February 14, 2025 1:00-4:00pm PST</p>
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<p><a href="https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-6">Intermediate
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<p><a href="https://gladstone.org/events/introduction-rna-seq-0">Introduction
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to RNA-Seq</a><br />
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May 12-May 13, 2025 1:00-4:00pm PDT</p>
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<p><a href="https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-7">Intermediate
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RNA-Seq Analysis Using R</a><br />
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February 20, 2025 9:00am-12:00pm PST</p>
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May 19, 2025 1:00-4:00pm PDT</p>
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<ul>
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<li>Check <a href="https://gladstone.org/events?series=data-science-training-program">this
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link</a> at for the full schedule</li>
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|
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@ -3,7 +3,7 @@
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<head>
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<meta charset="utf-8">
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<meta name="generator" content="pandoc">
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<meta name="author" content="Natalie Elphick" />
|
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<meta name="author" content="Natalie Gill" />
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<title>Introduction to R Data Analysis</title>
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<meta name="apple-mobile-web-app-capable" content="yes">
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<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
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@ -2795,8 +2795,8 @@ border: 0;
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<section>
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<h1 class="title">Introduction to R Data Analysis</h1>
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<h1 class="subtitle">Part 2</h1>
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<h2 class="author">Natalie Elphick</h2>
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<h3 class="date">January 28th, 2025</h3>
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<h2 class="author">Natalie Gill</h2>
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<h3 class="date">May 6th, 2025</h3>
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</section>
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<section id="section" class="slide level2">
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@ -2807,10 +2807,8 @@ border: 0;
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</section>
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<section id="introductions" class="title-slide slide level1">
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<h1>Introductions</h1>
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<p><strong>Natalie Elphick</strong><br />
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<p><strong>Natalie Gill</strong><br />
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Bioinformatician II</p>
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<p><strong>Min-Gyoung Shin</strong><br />
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Bioinformatician III</p>
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</section>
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<section id="schedule" class="title-slide slide level1">
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@ -2820,7 +2818,7 @@ Bioinformatician III</p>
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<li>Filtering and reformatting data</li>
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<li>Plotting data</li>
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<li>Hands on data analysis</li>
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<li>ChatGPT tips for R</li>
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<li>AI tips for R</li>
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<li>Where to get help</li>
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</ol>
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</section>
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@ -3046,7 +3044,7 @@ modified by adding layers</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_7cb781c7" 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_ed7c8eb5" 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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</ul>
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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 id="ai-tips-for-r" class="title-slide slide level1">
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<h1>AI 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>Follow any relevant institutional guidelines on using LLMs</li>
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<li>Always confirm ChatGPT’s outputs are correct</li>
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<li>Always confirm the 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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|
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@ -4274,7 +4272,7 @@ prompt</li>
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<ul>
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<li>Commented R code yields better responses</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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<li>LLMs 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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|
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@ -4364,15 +4362,12 @@ survey</a> so we can continue to improve these workshops</li>
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</section>
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<section id="upcoming-workshops" class="slide level2">
|
||||
<h2>Upcoming Workshops</h2>
|
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<p><a href="https://gladstone.org/events/introduction-unix-command-line-2">Introduction
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to Unix Command Line</a><br />
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February 10-February 11, 2025 1:00-3:00pm PST</p>
|
||||
<p><a href="https://gladstone.org/events/introduction-rna-seq-analysis-8">Introduction
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to RNA-Seq Analysis</a><br />
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February 13-February 14, 2025 1:00-4:00pm PST</p>
|
||||
<p><a href="https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-6">Intermediate
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<p><a href="https://gladstone.org/events/introduction-rna-seq-0">Introduction
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to RNA-Seq</a><br />
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May 12-May 13, 2025 1:00-4:00pm PDT</p>
|
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<p><a href="https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-7">Intermediate
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RNA-Seq Analysis Using R</a><br />
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February 20, 2025 9:00am-12:00pm PST</p>
|
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May 19, 2025 1:00-4:00pm PDT</p>
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<ul>
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<li>Check <a href="https://gladstone.org/events?series=data-science-training-program">this
|
||||
link</a> at for the full schedule</li>
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||||
|
|
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|||
|
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@ -1,8 +1,8 @@
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---
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title: "Introduction to R Data Analysis"
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subtitle: "Part 1"
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author: "Natalie Elphick"
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date: "January 27th, 2025"
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author: "Natalie Gill"
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date: "May 5th, 2025"
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knit: (function(input, ...) {
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rmarkdown::render(
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input,
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@ -26,13 +26,9 @@ knitr::opts_chunk$set(comment = "")
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## Introductions
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**Natalie Elphick**
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**Natalie Gill**
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Bioinformatician II
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**Michela Traglia**
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Senior Statistician
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## Poll 1
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@ -83,7 +79,7 @@ Keep at it—progress comes with persistence!
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## R
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- An open source language developed for statistical computing by **R**oss Ihaka and **R**obert Gentleman
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- Inspired by the **S** language developed at Bell labs in 1976 to make interactive data analysis easier
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- Developed at Bell labs in 1976 to make interactive data analysis easier
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- The first official version was released in 2000
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## Why use R for data analysis?
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@ -266,7 +262,7 @@ NA + 1
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1. "1.5" - Numeric
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2. "A" - Character
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3. 1L - Integer
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4. TRUE - Boolean
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4. TRUE - Boolean/Logical
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@ -466,7 +462,7 @@ packages
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## Why use Tidyverse Packages?
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- Most of the work in data analysis is getting data into the correct format to create outputs (plots and tables)
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- Much of the work in data analysis is getting data into the correct format to create outputs (plots and tables)
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- The tidyverse collection of packages simplifies this process
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- Intuitive syntax
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- Comprehensive (data manipulation, cleaning, modeling and graphics)
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@ -476,19 +472,30 @@ packages
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# End of Part 1
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## Schedule for Part 2
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1. Introduction to Tidyverse
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2. Filtering and reformatting data
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3. Plotting data
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4. Hands on data analysis
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5. AI tips for R
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6. Where to get help
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## Workshop survey
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- Please fill out our [workshop survey](https://www.surveymonkey.com/r/bioinfo-training) so we can continue to improve these workshops
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## Upcoming Workshops
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[Introduction to Unix Command Line](https://gladstone.org/events/introduction-unix-command-line-2)
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February 10-February 11, 2025 1:00-3:00pm PST
|
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[Introduction to RNA-Seq](https://gladstone.org/events/introduction-rna-seq-0)
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May 12-May 13, 2025 1:00-4:00pm PDT
|
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[Introduction to RNA-Seq Analysis](https://gladstone.org/events/introduction-rna-seq-analysis-8)
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February 13-February 14, 2025 1:00-4:00pm PST
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|
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[Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-6)
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February 20, 2025 9:00am-12:00pm PST
|
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[Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-7)
|
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May 19, 2025 1:00-4:00pm PDT
|
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|
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|
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- Check [this link](https://gladstone.org/events?series=data-science-training-program) at for the full schedule
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|
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|
|
|
|||
|
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@ -1,8 +1,8 @@
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---
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title: "Introduction to R Data Analysis"
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subtitle: "Part 2"
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author: "Natalie Elphick"
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date: "January 28th, 2025"
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author: "Natalie Gill"
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date: "May 6th, 2025"
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knit: (function(input, ...) {
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rmarkdown::render(
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input,
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@ -28,11 +28,9 @@ knitr::opts_chunk$set(comment = "")
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<center>*Press the ? key for tips on navigating these slides*</center>
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# Introductions
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**Natalie Elphick**
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**Natalie Gill**
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Bioinformatician II
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**Min-Gyoung Shin**
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Bioinformatician III
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# Schedule
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@ -40,7 +38,7 @@ Bioinformatician III
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2. Filtering and reformatting data
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3. Plotting data
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4. Hands on data analysis
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5. ChatGPT tips for R
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5. AI tips for R
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6. Where to get help
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|
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@ -239,12 +237,13 @@ Steps:
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# ChatGPT Tips for R
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# AI Tips for R
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## General Tips
|
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|
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- Follow any relevant institutional guidelines on using LLMs
|
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- Always confirm ChatGPT's outputs are correct
|
||||
- Always confirm the outputs are correct
|
||||
- Provide as much detail as possible about the problem in the 1st prompt
|
||||
- Use separate chats for separate tasks/projects
|
||||
- Try the 'Custom Instructions' function
|
||||
|
|
@ -253,7 +252,7 @@ Steps:
|
|||
|
||||
- Commented R code yields better responses
|
||||
- Provide the code and error message in the same prompt
|
||||
- ChatGPT can work well to convert syntax and improve your code:
|
||||
- LLMs can work well to convert syntax and improve your code:
|
||||
- "Turn this loop into a function : [your code]"
|
||||
- "Is there a better way to do this : [your code]"
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- Check out the file: `example_code/1_convert_syntax_example.R` for an example use case
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@ -306,14 +305,12 @@ Code templates can be used to avoid typing the same code over and over again.
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## Upcoming Workshops
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||||
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||||
[Introduction to Unix Command Line](https://gladstone.org/events/introduction-unix-command-line-2)
|
||||
February 10-February 11, 2025 1:00-3:00pm PST
|
||||
[Introduction to RNA-Seq](https://gladstone.org/events/introduction-rna-seq-0)
|
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May 12-May 13, 2025 1:00-4:00pm PDT
|
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|
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[Introduction to RNA-Seq Analysis](https://gladstone.org/events/introduction-rna-seq-analysis-8)
|
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February 13-February 14, 2025 1:00-4:00pm PST
|
||||
[Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-7)
|
||||
May 19, 2025 1:00-4:00pm PDT
|
||||
|
||||
[Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-6)
|
||||
February 20, 2025 9:00am-12:00pm PST
|
||||
|
||||
- Check [this link](https://gladstone.org/events?series=data-science-training-program) at for the full schedule
|
||||
|
||||
|
|
|
|||
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Reference in a new issue