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44
docs/Intro_to_R_data_analysis_part_1.html
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@ -3,7 +3,7 @@
<head> <head>
<meta charset="utf-8"> <meta charset="utf-8">
<meta name="generator" content="pandoc"> <meta name="generator" content="pandoc">
<meta name="author" content="Natalie Elphick" /> <meta name="author" content="Natalie Gill" />
<title>Introduction to R Data Analysis</title> <title>Introduction to R Data Analysis</title>
<meta name="apple-mobile-web-app-capable" content="yes"> <meta name="apple-mobile-web-app-capable" content="yes">
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent"> <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
@ -2571,8 +2571,8 @@ class CountdownTimer {
<section> <section>
<h1 class="title">Introduction to R Data Analysis</h1> <h1 class="title">Introduction to R Data Analysis</h1>
<h1 class="subtitle">Part 1</h1> <h1 class="subtitle">Part 1</h1>
<h2 class="author">Natalie Elphick</h2> <h2 class="author">Natalie Gill</h2>
<h3 class="date">January 27th, 2025</h3> <h3 class="date">May 5th, 2025</h3>
</section> </section>
<section id="section" class="slide level2"> <section id="section" class="slide level2">
@ -2583,10 +2583,8 @@ class CountdownTimer {
</section> </section>
<section id="introductions" class="slide level2"> <section id="introductions" class="slide level2">
<h2>Introductions</h2> <h2>Introductions</h2>
<p><strong>Natalie Elphick</strong><br /> <p><strong>Natalie Gill</strong><br />
Bioinformatician II</p> Bioinformatician II</p>
<p><strong>Michela Traglia</strong><br />
Senior Statistician</p>
</section> </section>
<section id="poll-1" class="slide level2"> <section id="poll-1" class="slide level2">
<h2>Poll 1</h2> <h2>Poll 1</h2>
@ -2652,8 +2650,8 @@ the end of the workshop to continue at your own pace.</li>
<ul> <ul>
<li>An open source language developed for statistical computing by <li>An open source language developed for statistical computing by
<strong>R</strong>oss Ihaka and <strong>R</strong>obert Gentleman</li> <strong>R</strong>oss Ihaka and <strong>R</strong>obert Gentleman</li>
<li>Inspired by the <strong>S</strong> language developed at Bell labs <li>Developed at Bell labs in 1976 to make interactive data analysis
in 1976 to make interactive data analysis easier</li> easier</li>
<li>The first official version was released in 2000</li> <li>The first official version was released in 2000</li>
</ul> </ul>
</section> </section>
@ -2883,7 +2881,7 @@ value?</strong></p>
<li>“1.5” - Numeric</li> <li>“1.5” - Numeric</li>
<li>“A” - Character</li> <li>“A” - Character</li>
<li>1L - Integer</li> <li>1L - Integer</li>
<li>TRUE - Boolean</li> <li>TRUE - Boolean/Logical</li>
</ol> </ol>
</section> </section>
<section id="data-structures" class="slide level2"> <section id="data-structures" class="slide level2">
@ -2923,7 +2921,7 @@ types/structures</strong> (ex. nested lists)</li>
<section id="min-break" class="title-slide slide level1"> <section id="min-break" class="title-slide slide level1">
<h1>10 min break</h1> <h1>10 min break</h1>
<center> <center>
<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;"> <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;">
<div class="countdown-controls"><button class="countdown-bump-down">−</button><button class="countdown-bump-up">+</button></div> <div class="countdown-controls"><button class="countdown-bump-down">−</button><button class="countdown-bump-up">+</button></div>
<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> <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>
</div> </div>
@ -3092,7 +3090,7 @@ correct format</li>
<section id="why-use-tidyverse-packages" class="slide level2"> <section id="why-use-tidyverse-packages" class="slide level2">
<h2>Why use Tidyverse Packages?</h2> <h2>Why use Tidyverse Packages?</h2>
<ul> <ul>
<li>Most of the work in data analysis is getting data into the correct <li>Much of the work in data analysis is getting data into the correct
format to create outputs (plots and tables)</li> format to create outputs (plots and tables)</li>
<li>The tidyverse collection of packages simplifies this process <li>The tidyverse collection of packages simplifies this process
<ul> <ul>
@ -3108,6 +3106,17 @@ graphics)</li>
<section id="end-of-part-1" class="title-slide slide level1"> <section id="end-of-part-1" class="title-slide slide level1">
<h1>End of Part 1</h1> <h1>End of Part 1</h1>
</section>
<section id="schedule-for-part-2" class="slide level2">
<h2>Schedule for Part 2</h2>
<ol type="1">
<li>Introduction to Tidyverse</li>
<li>Filtering and reformatting data</li>
<li>Plotting data</li>
<li>Hands on data analysis</li>
<li>AI tips for R</li>
<li>Where to get help</li>
</ol>
</section> </section>
<section id="workshop-survey" class="slide level2"> <section id="workshop-survey" class="slide level2">
<h2>Workshop survey</h2> <h2>Workshop survey</h2>
@ -3118,15 +3127,12 @@ survey</a> so we can continue to improve these workshops</li>
</section> </section>
<section id="upcoming-workshops" class="slide level2"> <section id="upcoming-workshops" class="slide level2">
<h2>Upcoming Workshops</h2> <h2>Upcoming Workshops</h2>
<p><a href="https://gladstone.org/events/introduction-unix-command-line-2">Introduction <p><a href="https://gladstone.org/events/introduction-rna-seq-0">Introduction
to Unix Command Line</a><br /> to RNA-Seq</a><br />
February 10-February 11, 2025 1:00-3:00pm PST</p> May 12-May 13, 2025 1:00-4:00pm PDT</p>
<p><a href="https://gladstone.org/events/introduction-rna-seq-analysis-8">Introduction <p><a href="https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-7">Intermediate
to RNA-Seq Analysis</a><br />
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
RNA-Seq Analysis Using R</a><br /> RNA-Seq Analysis Using R</a><br />
February 20, 2025 9:00am-12:00pm PST</p> May 19, 2025 1:00-4:00pm PDT</p>
<ul> <ul>
<li>Check <a href="https://gladstone.org/events?series=data-science-training-program">this <li>Check <a href="https://gladstone.org/events?series=data-science-training-program">this
link</a> at for the full schedule</li> link</a> at for the full schedule</li>

35
docs/Intro_to_R_data_analysis_part_2.html
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@ -3,7 +3,7 @@
<head> <head>
<meta charset="utf-8"> <meta charset="utf-8">
<meta name="generator" content="pandoc"> <meta name="generator" content="pandoc">
<meta name="author" content="Natalie Elphick" /> <meta name="author" content="Natalie Gill" />
<title>Introduction to R Data Analysis</title> <title>Introduction to R Data Analysis</title>
<meta name="apple-mobile-web-app-capable" content="yes"> <meta name="apple-mobile-web-app-capable" content="yes">
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent"> <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
@ -2795,8 +2795,8 @@ border: 0;
<section> <section>
<h1 class="title">Introduction to R Data Analysis</h1> <h1 class="title">Introduction to R Data Analysis</h1>
<h1 class="subtitle">Part 2</h1> <h1 class="subtitle">Part 2</h1>
<h2 class="author">Natalie Elphick</h2> <h2 class="author">Natalie Gill</h2>
<h3 class="date">January 28th, 2025</h3> <h3 class="date">May 6th, 2025</h3>
</section> </section>
<section id="section" class="slide level2"> <section id="section" class="slide level2">
@ -2807,10 +2807,8 @@ border: 0;
</section> </section>
<section id="introductions" class="title-slide slide level1"> <section id="introductions" class="title-slide slide level1">
<h1>Introductions</h1> <h1>Introductions</h1>
<p><strong>Natalie Elphick</strong><br /> <p><strong>Natalie Gill</strong><br />
Bioinformatician II</p> Bioinformatician II</p>
<p><strong>Min-Gyoung Shin</strong><br />
Bioinformatician III</p>
</section> </section>
<section id="schedule" class="title-slide slide level1"> <section id="schedule" class="title-slide slide level1">
@ -2820,7 +2818,7 @@ Bioinformatician III</p>
<li>Filtering and reformatting data</li> <li>Filtering and reformatting data</li>
<li>Plotting data</li> <li>Plotting data</li>
<li>Hands on data analysis</li> <li>Hands on data analysis</li>
<li>ChatGPT tips for R</li> <li>AI tips for R</li>
<li>Where to get help</li> <li>Where to get help</li>
</ol> </ol>
</section> </section>
@ -3046,7 +3044,7 @@ modified by adding layers</li>
<section id="min-break" class="title-slide slide level1"> <section id="min-break" class="title-slide slide level1">
<h1>10 min break</h1> <h1>10 min break</h1>
<center> <center>
<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;"> <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;">
<div class="countdown-controls"><button class="countdown-bump-down">−</button><button class="countdown-bump-up">+</button></div> <div class="countdown-controls"><button class="countdown-bump-down">−</button><button class="countdown-bump-up">+</button></div>
<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> <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>
</div> </div>
@ -4254,15 +4252,15 @@ part2_filled_out.html</li>
</ul> </ul>
</section></section> </section></section>
<section> <section>
<section id="chatgpt-tips-for-r" class="title-slide slide level1"> <section id="ai-tips-for-r" class="title-slide slide level1">
<h1>ChatGPT Tips for R</h1> <h1>AI Tips for R</h1>
</section> </section>
<section id="general-tips" class="slide level2"> <section id="general-tips" class="slide level2">
<h2>General Tips</h2> <h2>General Tips</h2>
<ul> <ul>
<li>Follow any relevant institutional guidelines on using LLMs</li> <li>Follow any relevant institutional guidelines on using LLMs</li>
<li>Always confirm ChatGPT’s outputs are correct</li> <li>Always confirm the outputs are correct</li>
<li>Provide as much detail as possible about the problem in the 1st <li>Provide as much detail as possible about the problem in the 1st
prompt</li> prompt</li>
<li>Use separate chats for separate tasks/projects</li> <li>Use separate chats for separate tasks/projects</li>
@ -4274,7 +4272,7 @@ prompt</li>
<ul> <ul>
<li>Commented R code yields better responses</li> <li>Commented R code yields better responses</li>
<li>Provide the code and error message in the same prompt</li> <li>Provide the code and error message in the same prompt</li>
<li>ChatGPT can work well to convert syntax and improve your code: <li>LLMs can work well to convert syntax and improve your code:
<ul> <ul>
<li>“Turn this loop into a function : [your code]”</li> <li>“Turn this loop into a function : [your code]”</li>
<li>“Is there a better way to do this : [your code]”</li> <li>“Is there a better way to do this : [your code]”</li>
@ -4364,15 +4362,12 @@ survey</a> so we can continue to improve these workshops</li>
</section> </section>
<section id="upcoming-workshops" class="slide level2"> <section id="upcoming-workshops" class="slide level2">
<h2>Upcoming Workshops</h2> <h2>Upcoming Workshops</h2>
<p><a href="https://gladstone.org/events/introduction-unix-command-line-2">Introduction <p><a href="https://gladstone.org/events/introduction-rna-seq-0">Introduction
to Unix Command Line</a><br /> to RNA-Seq</a><br />
February 10-February 11, 2025 1:00-3:00pm PST</p> May 12-May 13, 2025 1:00-4:00pm PDT</p>
<p><a href="https://gladstone.org/events/introduction-rna-seq-analysis-8">Introduction <p><a href="https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-7">Intermediate
to RNA-Seq Analysis</a><br />
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
RNA-Seq Analysis Using R</a><br /> RNA-Seq Analysis Using R</a><br />
February 20, 2025 9:00am-12:00pm PST</p> May 19, 2025 1:00-4:00pm PDT</p>
<ul> <ul>
<li>Check <a href="https://gladstone.org/events?series=data-science-training-program">this <li>Check <a href="https://gladstone.org/events?series=data-science-training-program">this
link</a> at for the full schedule</li> link</a> at for the full schedule</li>

39
intro-r-data-analysis/Intro_to_R_data_analysis_part_1.Rmd
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@ -1,8 +1,8 @@
--- ---
title: "Introduction to R Data Analysis" title: "Introduction to R Data Analysis"
subtitle: "Part 1" subtitle: "Part 1"
author: "Natalie Elphick" author: "Natalie Gill"
date: "January 27th, 2025" date: "May 5th, 2025"
knit: (function(input, ...) { knit: (function(input, ...) {
rmarkdown::render( rmarkdown::render(
input, input,
@ -26,13 +26,9 @@ knitr::opts_chunk$set(comment = "")
## Introductions ## Introductions
**Natalie Elphick** **Natalie Gill**
Bioinformatician II Bioinformatician II
**Michela Traglia**
Senior Statistician
## Poll 1 ## Poll 1
@ -83,7 +79,7 @@ Keep at it—progress comes with persistence!
## R ## R
- An open source language developed for statistical computing by **R**oss Ihaka and **R**obert Gentleman - An open source language developed for statistical computing by **R**oss Ihaka and **R**obert Gentleman
- Inspired by the **S** language developed at Bell labs in 1976 to make interactive data analysis easier - Developed at Bell labs in 1976 to make interactive data analysis easier
- The first official version was released in 2000 - The first official version was released in 2000
## Why use R for data analysis? ## Why use R for data analysis?
@ -266,7 +262,7 @@ NA + 1
1. "1.5" - Numeric 1. "1.5" - Numeric
2. "A" - Character 2. "A" - Character
3. 1L - Integer 3. 1L - Integer
4. TRUE - Boolean 4. TRUE - Boolean/Logical
@ -466,7 +462,7 @@ packages
## Why use Tidyverse Packages? ## Why use Tidyverse Packages?
- Most of the work in data analysis is getting data into the correct format to create outputs (plots and tables) - Much of the work in data analysis is getting data into the correct format to create outputs (plots and tables)
- The tidyverse collection of packages simplifies this process - The tidyverse collection of packages simplifies this process
- Intuitive syntax - Intuitive syntax
- Comprehensive (data manipulation, cleaning, modeling and graphics) - Comprehensive (data manipulation, cleaning, modeling and graphics)
@ -476,19 +472,30 @@ packages
# End of Part 1 # End of Part 1
## Schedule for Part 2
1. Introduction to Tidyverse
2. Filtering and reformatting data
3. Plotting data
4. Hands on data analysis
5. AI tips for R
6. Where to get help
## Workshop survey ## Workshop survey
- Please fill out our [workshop survey](https://www.surveymonkey.com/r/bioinfo-training) so we can continue to improve these workshops - Please fill out our [workshop survey](https://www.surveymonkey.com/r/bioinfo-training) so we can continue to improve these workshops
## Upcoming Workshops ## Upcoming Workshops
[Introduction to Unix Command Line](https://gladstone.org/events/introduction-unix-command-line-2) [Introduction to RNA-Seq](https://gladstone.org/events/introduction-rna-seq-0)
February 10-February 11, 2025 1:00-3:00pm PST May 12-May 13, 2025 1:00-4:00pm PDT
[Introduction to RNA-Seq Analysis](https://gladstone.org/events/introduction-rna-seq-analysis-8)
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-6) [Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-7)
February 20, 2025 9:00am-12:00pm PST May 19, 2025 1:00-4:00pm PDT
- Check [this link](https://gladstone.org/events?series=data-science-training-program) at for the full schedule - Check [this link](https://gladstone.org/events?series=data-science-training-program) at for the full schedule

27
intro-r-data-analysis/Intro_to_R_data_analysis_part_2.Rmd
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@ -1,8 +1,8 @@
--- ---
title: "Introduction to R Data Analysis" title: "Introduction to R Data Analysis"
subtitle: "Part 2" subtitle: "Part 2"
author: "Natalie Elphick" author: "Natalie Gill"
date: "January 28th, 2025" date: "May 6th, 2025"
knit: (function(input, ...) { knit: (function(input, ...) {
rmarkdown::render( rmarkdown::render(
input, input,
@ -28,11 +28,9 @@ knitr::opts_chunk$set(comment = "")
<center>*Press the ? key for tips on navigating these slides*</center> <center>*Press the ? key for tips on navigating these slides*</center>
# Introductions # Introductions
**Natalie Elphick** **Natalie Gill**
Bioinformatician II Bioinformatician II
**Min-Gyoung Shin**
Bioinformatician III
# Schedule # Schedule
@ -40,7 +38,7 @@ Bioinformatician III
2. Filtering and reformatting data 2. Filtering and reformatting data
3. Plotting data 3. Plotting data
4. Hands on data analysis 4. Hands on data analysis
5. ChatGPT tips for R 5. AI tips for R
6. Where to get help 6. Where to get help
@ -239,12 +237,13 @@ Steps:
# ChatGPT Tips for R # AI Tips for R
## General Tips ## General Tips
- Follow any relevant institutional guidelines on using LLMs - Follow any relevant institutional guidelines on using LLMs
- 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 - Provide as much detail as possible about the problem in the 1st prompt
- Use separate chats for separate tasks/projects - Use separate chats for separate tasks/projects
- Try the 'Custom Instructions' function - Try the 'Custom Instructions' function
@ -253,7 +252,7 @@ Steps:
- Commented R code yields better responses - Commented R code yields better responses
- Provide the code and error message in the same prompt - 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]" - "Turn this loop into a function : [your code]"
- "Is there a better way to do this : [your code]" - "Is there a better way to do this : [your code]"
- Check out the file: `example_code/1_convert_syntax_example.R` for an example use case - Check out the file: `example_code/1_convert_syntax_example.R` for an example use case
@ -306,14 +305,12 @@ Code templates can be used to avoid typing the same code over and over again.
## Upcoming Workshops ## Upcoming Workshops
[Introduction to Unix Command Line](https://gladstone.org/events/introduction-unix-command-line-2) [Introduction to RNA-Seq](https://gladstone.org/events/introduction-rna-seq-0)
February 10-February 11, 2025 1:00-3:00pm PST May 12-May 13, 2025 1:00-4:00pm PDT
[Introduction to RNA-Seq Analysis](https://gladstone.org/events/introduction-rna-seq-analysis-8) [Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-7)
February 13-February 14, 2025 1:00-4:00pm PST 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 - Check [this link](https://gladstone.org/events?series=data-science-training-program) at for the full schedule