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44
docs/Intro_to_R_data_analysis_part_1.html
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@ -3,7 +3,7 @@
<head>
<meta charset="utf-8">
<meta name="generator" content="pandoc">
<meta name="author" content="Natalie Elphick" />
<meta name="author" content="Natalie Gill" />
<title>Introduction to R Data Analysis</title>
<meta name="apple-mobile-web-app-capable" content="yes">
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
@ -2571,8 +2571,8 @@ class CountdownTimer {
<section>
<h1 class="title">Introduction to R Data Analysis</h1>
<h1 class="subtitle">Part 1</h1>
<h2 class="author">Natalie Elphick</h2>
<h3 class="date">January 27th, 2025</h3>
<h2 class="author">Natalie Gill</h2>
<h3 class="date">May 5th, 2025</h3>
</section>
<section id="section" class="slide level2">
@ -2583,10 +2583,8 @@ class CountdownTimer {
</section>
<section id="introductions" class="slide level2">
<h2>Introductions</h2>
<p><strong>Natalie Elphick</strong><br />
<p><strong>Natalie Gill</strong><br />
Bioinformatician II</p>
<p><strong>Michela Traglia</strong><br />
Senior Statistician</p>
</section>
<section id="poll-1" class="slide level2">
<h2>Poll 1</h2>
@ -2652,8 +2650,8 @@ the end of the workshop to continue at your own pace.</li>
<ul>
<li>An open source language developed for statistical computing by
<strong>R</strong>oss Ihaka and <strong>R</strong>obert Gentleman</li>
<li>Inspired by the <strong>S</strong> language developed at Bell labs
in 1976 to make interactive data analysis easier</li>
<li>Developed at Bell labs in 1976 to make interactive data analysis
easier</li>
<li>The first official version was released in 2000</li>
</ul>
</section>
@ -2883,7 +2881,7 @@ value?</strong></p>
<li>“1.5” - Numeric</li>
<li>“A” - Character</li>
<li>1L - Integer</li>
<li>TRUE - Boolean</li>
<li>TRUE - Boolean/Logical</li>
</ol>
</section>
<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">
<h1>10 min break</h1>
<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>
<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>
@ -3092,7 +3090,7 @@ correct format</li>
<section id="why-use-tidyverse-packages" class="slide level2">
<h2>Why use Tidyverse Packages?</h2>
<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>
<li>The tidyverse collection of packages simplifies this process
<ul>
@ -3108,6 +3106,17 @@ graphics)</li>
<section id="end-of-part-1" class="title-slide slide level1">
<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 id="workshop-survey" class="slide level2">
<h2>Workshop survey</h2>
@ -3118,15 +3127,12 @@ survey</a> so we can continue to improve these workshops</li>
</section>
<section id="upcoming-workshops" class="slide level2">
<h2>Upcoming Workshops</h2>
<p><a href="https://gladstone.org/events/introduction-unix-command-line-2">Introduction
to Unix Command Line</a><br />
February 10-February 11, 2025 1:00-3:00pm PST</p>
<p><a href="https://gladstone.org/events/introduction-rna-seq-analysis-8">Introduction
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
<p><a href="https://gladstone.org/events/introduction-rna-seq-0">Introduction
to RNA-Seq</a><br />
May 12-May 13, 2025 1:00-4:00pm PDT</p>
<p><a href="https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-7">Intermediate
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>
<li>Check <a href="https://gladstone.org/events?series=data-science-training-program">this
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>
<meta charset="utf-8">
<meta name="generator" content="pandoc">
<meta name="author" content="Natalie Elphick" />
<meta name="author" content="Natalie Gill" />
<title>Introduction to R Data Analysis</title>
<meta name="apple-mobile-web-app-capable" content="yes">
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
@ -2795,8 +2795,8 @@ border: 0;
<section>
<h1 class="title">Introduction to R Data Analysis</h1>
<h1 class="subtitle">Part 2</h1>
<h2 class="author">Natalie Elphick</h2>
<h3 class="date">January 28th, 2025</h3>
<h2 class="author">Natalie Gill</h2>
<h3 class="date">May 6th, 2025</h3>
</section>
<section id="section" class="slide level2">
@ -2807,10 +2807,8 @@ border: 0;
</section>
<section id="introductions" class="title-slide slide level1">
<h1>Introductions</h1>
<p><strong>Natalie Elphick</strong><br />
<p><strong>Natalie Gill</strong><br />
Bioinformatician II</p>
<p><strong>Min-Gyoung Shin</strong><br />
Bioinformatician III</p>
</section>
<section id="schedule" class="title-slide slide level1">
@ -2820,7 +2818,7 @@ Bioinformatician III</p>
<li>Filtering and reformatting data</li>
<li>Plotting data</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>
</ol>
</section>
@ -3046,7 +3044,7 @@ modified by adding layers</li>
<section id="min-break" class="title-slide slide level1">
<h1>10 min break</h1>
<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>
<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>
@ -4254,15 +4252,15 @@ part2_filled_out.html</li>
</ul>
</section></section>
<section>
<section id="chatgpt-tips-for-r" class="title-slide slide level1">
<h1>ChatGPT Tips for R</h1>
<section id="ai-tips-for-r" class="title-slide slide level1">
<h1>AI Tips for R</h1>
</section>
<section id="general-tips" class="slide level2">
<h2>General Tips</h2>
<ul>
<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
prompt</li>
<li>Use separate chats for separate tasks/projects</li>
@ -4274,7 +4272,7 @@ prompt</li>
<ul>
<li>Commented R code yields better responses</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>
<li>“Turn this loop into a function : [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 id="upcoming-workshops" class="slide level2">
<h2>Upcoming Workshops</h2>
<p><a href="https://gladstone.org/events/introduction-unix-command-line-2">Introduction
to Unix Command Line</a><br />
February 10-February 11, 2025 1:00-3:00pm PST</p>
<p><a href="https://gladstone.org/events/introduction-rna-seq-analysis-8">Introduction
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
<p><a href="https://gladstone.org/events/introduction-rna-seq-0">Introduction
to RNA-Seq</a><br />
May 12-May 13, 2025 1:00-4:00pm PDT</p>
<p><a href="https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-7">Intermediate
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>
<li>Check <a href="https://gladstone.org/events?series=data-science-training-program">this
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"
subtitle: "Part 1"
author: "Natalie Elphick"
date: "January 27th, 2025"
author: "Natalie Gill"
date: "May 5th, 2025"
knit: (function(input, ...) {
rmarkdown::render(
input,
@ -26,13 +26,9 @@ knitr::opts_chunk$set(comment = "")
## Introductions
**Natalie Elphick**
**Natalie Gill**
Bioinformatician II
**Michela Traglia**
Senior Statistician
## Poll 1
@ -83,7 +79,7 @@ Keep at it—progress comes with persistence!
## R
- 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
## Why use R for data analysis?
@ -266,7 +262,7 @@ NA + 1
1. "1.5" - Numeric
2. "A" - Character
3. 1L - Integer
4. TRUE - Boolean
4. TRUE - Boolean/Logical
@ -466,7 +462,7 @@ 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
- Intuitive syntax
- Comprehensive (data manipulation, cleaning, modeling and graphics)
@ -476,19 +472,30 @@ packages
# 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
- Please fill out our [workshop survey](https://www.surveymonkey.com/r/bioinfo-training) so we can continue to improve these workshops
## Upcoming Workshops
[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)
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)
February 20, 2025 9:00am-12:00pm 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
- 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
View file

@ -1,8 +1,8 @@
---
title: "Introduction to R Data Analysis"
subtitle: "Part 2"
author: "Natalie Elphick"
date: "January 28th, 2025"
author: "Natalie Gill"
date: "May 6th, 2025"
knit: (function(input, ...) {
rmarkdown::render(
input,
@ -28,11 +28,9 @@ knitr::opts_chunk$set(comment = "")
<center>*Press the ? key for tips on navigating these slides*</center>
# Introductions
**Natalie Elphick**
**Natalie Gill**
Bioinformatician II
**Min-Gyoung Shin**
Bioinformatician III
# Schedule
@ -40,7 +38,7 @@ Bioinformatician III
2. Filtering and reformatting data
3. Plotting data
4. Hands on data analysis
5. ChatGPT tips for R
5. AI tips for R
6. Where to get help
@ -239,12 +237,13 @@ Steps:
# ChatGPT Tips for R
# AI Tips for R
## General Tips
- 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
- 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]"
- 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
[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)
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-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