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docs/Intro_to_R_data_analysis_part_1.html
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@ -2572,7 +2572,7 @@ class CountdownTimer {
<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 Elphick</h2>
<h3 class="date">November 11th, 2024</h3> <h3 class="date">January 27th, 2025</h3>
</section> </section>
<section id="section" class="slide level2"> <section id="section" class="slide level2">
@ -2584,7 +2584,9 @@ class CountdownTimer {
<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 Elphick</strong><br />
Bioinformatician I</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>
@ -2921,7 +2923,7 @@ 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_1fd2ccf2" 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_d165775b" 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>
@ -3091,7 +3093,7 @@ correct format</li>
<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>Most of the work in data analysis is getting data into the correct
format to create outputs</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>
<li>Intuitive syntax</li> <li>Intuitive syntax</li>
@ -3110,21 +3112,21 @@ graphics)</li>
<section id="workshop-survey" class="slide level2"> <section id="workshop-survey" class="slide level2">
<h2>Workshop survey</h2> <h2>Workshop survey</h2>
<ul> <ul>
<li>Please fill out our <a href="https://www.surveymonkey.com/r/F75J6VZ">workshop survey</a> so we <li>Please fill out our <a href="https://www.surveymonkey.com/r/bioinfo-training">workshop
can continue to improve these workshops</li> survey</a> so we can continue to improve these workshops</li>
</ul> </ul>
</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-scatac-seq-data-analysis">Introduction <p><a href="https://gladstone.org/events/introduction-unix-command-line-2">Introduction
to scATAC-seq Data Analysis</a><br /> to Unix Command Line</a><br />
November 14 - November 15, 2024 1:00-4:00pm PST</p> February 10-February 11, 2025 1:00-3:00pm PST</p>
<p><a href="https://gladstone.org/events/introduction-linear-mixed-effects-models-0">Introduction <p><a href="https://gladstone.org/events/introduction-rna-seq-analysis-8">Introduction
to Linear Mixed Effects Models</a><br /> to RNA-Seq Analysis</a><br />
November 18-November 19, 2024 1:00-3:00pm PST</p> February 13-February 14, 2025 1:00-4:00pm PST</p>
<p><a href="https://gladstone.org/events/scatac-seq-and-scrna-seq-data-integration">scATAC-seq <p><a href="https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-6">Intermediate
and scRNA-seq Data Integration</a><br /> RNA-Seq Analysis Using R</a><br />
November 22, 2024 1:00-4:00pm PST</p> February 20, 2025 9:00am-12:00pm PST</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>

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docs/Intro_to_R_data_analysis_part_2.html
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intro-r-data-analysis/Intro_to_R_data_analysis_part_1.Rmd
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@ -2,7 +2,7 @@
title: "Introduction to R Data Analysis" title: "Introduction to R Data Analysis"
subtitle: "Part 1" subtitle: "Part 1"
author: "Natalie Elphick" author: "Natalie Elphick"
date: "November 11th, 2024" date: "January 27th, 2025"
knit: (function(input, ...) { knit: (function(input, ...) {
rmarkdown::render( rmarkdown::render(
input, input,
@ -27,8 +27,10 @@ knitr::opts_chunk$set(comment = "")
## Introductions ## Introductions
**Natalie Elphick** **Natalie Elphick**
Bioinformatician I Bioinformatician II
**Michela Traglia**
Senior Statistician
@ -464,7 +466,7 @@ 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 - Most 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)
@ -475,19 +477,18 @@ packages
# End of Part 1 # End of Part 1
## Workshop survey ## Workshop survey
- Please fill out our [workshop survey](https://www.surveymonkey.com/r/F75J6VZ) 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 scATAC-seq Data Analysis](https://gladstone.org/events/introduction-scatac-seq-data-analysis) [Introduction to Unix Command Line](https://gladstone.org/events/introduction-unix-command-line-2)
November 14 - November 15, 2024 1:00-4:00pm PST February 10-February 11, 2025 1:00-3:00pm PST
[Introduction to Linear Mixed Effects Models](https://gladstone.org/events/introduction-linear-mixed-effects-models-0) [Introduction to RNA-Seq Analysis](https://gladstone.org/events/introduction-rna-seq-analysis-8)
November 18-November 19, 2024 1:00-3:00pm PST February 13-February 14, 2025 1:00-4:00pm PST
[scATAC-seq and scRNA-seq Data Integration](https://gladstone.org/events/scatac-seq-and-scrna-seq-data-integration)
November 22, 2024 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
- 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

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intro-r-data-analysis/Intro_to_R_data_analysis_part_2.Rmd
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@ -2,7 +2,7 @@
title: "Introduction to R Data Analysis" title: "Introduction to R Data Analysis"
subtitle: "Part 2" subtitle: "Part 2"
author: "Natalie Elphick" author: "Natalie Elphick"
date: "November 12th, 2024" date: "January 28th, 2025"
knit: (function(input, ...) { knit: (function(input, ...) {
rmarkdown::render( rmarkdown::render(
input, input,
@ -29,7 +29,7 @@ knitr::opts_chunk$set(comment = "")
# Introductions # Introductions
**Natalie Elphick** **Natalie Elphick**
Bioinformatician I Bioinformatician II
**Min-Gyoung Shin** **Min-Gyoung Shin**
Bioinformatician III Bioinformatician III
@ -282,10 +282,11 @@ For any bioinformatics specific questions feel free to reach out to the Gladston
Code templates can be used to avoid typing the same code over and over again. Code templates can be used to avoid typing the same code over and over again.
- These are templates that we are using to automate things like plot appearance and documentation: - These are templates can be used to automate things like plot appearance and documentation:
- [.Rmd Template](https://www.dropbox.com/scl/fi/a9cnyqdajgabbfcxbmm6y/RMD_template.Rmd?rlkey=yntfpo6aptw9b4pgjyzpe5ubi&dl=1) - [.Rmd Template](https://www.dropbox.com/scl/fi/a9cnyqdajgabbfcxbmm6y/RMD_template.Rmd?rlkey=yntfpo6aptw9b4pgjyzpe5ubi&dl=1)
- [.R Script Template](https://www.dropbox.com/scl/fi/cy43b8b1x3nzn17esnmmt/Rscript_template.R?rlkey=zn7b0g8nn0s9213blh70fjjsx&dl=1) - [.R Script Template](https://www.dropbox.com/scl/fi/cy43b8b1x3nzn17esnmmt/Rscript_template.R?rlkey=zn7b0g8nn0s9213blh70fjjsx&dl=1)
- Customize these for your use case to save time
## R Resources ## R Resources
@ -301,21 +302,21 @@ Code templates can be used to avoid typing the same code over and over again.
# End of Part 2 # End of Part 2
## Workshop survey ## Workshop survey
- Please fill out our [workshop survey](https://www.surveymonkey.com/r/F75J6VZ) 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 scATAC-seq Data Analysis](https://gladstone.org/events/introduction-scatac-seq-data-analysis) [Introduction to Unix Command Line](https://gladstone.org/events/introduction-unix-command-line-2)
November 14 - November 15, 2024 1:00-4:00pm PST February 10-February 11, 2025 1:00-3:00pm PST
[Introduction to Linear Mixed Effects Models](https://gladstone.org/events/introduction-linear-mixed-effects-models-0) [Introduction to RNA-Seq Analysis](https://gladstone.org/events/introduction-rna-seq-analysis-8)
November 18-November 19, 2024 1:00-3:00pm PST February 13-February 14, 2025 1:00-4:00pm PST
[scATAC-seq and scRNA-seq Data Integration](https://gladstone.org/events/scatac-seq-and-scrna-seq-data-integration)
November 22, 2024 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
- 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

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RestoreWorkspace: Default RestoreWorkspace: Default
SaveWorkspace: Default SaveWorkspace: Default