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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="subtitle">Part 1</h1>
<h2 class="author">Natalie Elphick</h2>
<h3 class="date">November 11th, 2024</h3>
<h3 class="date">January 27th, 2025</h3>
</section>
<section id="section" class="slide level2">
@ -2584,7 +2584,9 @@ class CountdownTimer {
<section id="introductions" class="slide level2">
<h2>Introductions</h2>
<p><strong>Natalie Elphick</strong><br />
Bioinformatician I</p>
Bioinformatician II</p>
<p><strong>Michela Traglia</strong><br />
Senior Statistician</p>
</section>
<section id="poll-1" class="slide level2">
<h2>Poll 1</h2>
@ -2921,7 +2923,7 @@ 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_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>
<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>
@ -3091,7 +3093,7 @@ correct format</li>
<h2>Why use Tidyverse Packages?</h2>
<ul>
<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
<ul>
<li>Intuitive syntax</li>
@ -3110,21 +3112,21 @@ graphics)</li>
<section id="workshop-survey" class="slide level2">
<h2>Workshop survey</h2>
<ul>
<li>Please fill out our <a href="https://www.surveymonkey.com/r/F75J6VZ">workshop survey</a> so we
can continue to improve these workshops</li>
<li>Please fill out our <a href="https://www.surveymonkey.com/r/bioinfo-training">workshop
survey</a> so we can continue to improve these workshops</li>
</ul>
</section>
<section id="upcoming-workshops" class="slide level2">
<h2>Upcoming Workshops</h2>
<p><a href="https://gladstone.org/events/introduction-scatac-seq-data-analysis">Introduction
to scATAC-seq Data Analysis</a><br />
November 14 - November 15, 2024 1:00-4:00pm PST</p>
<p><a href="https://gladstone.org/events/introduction-linear-mixed-effects-models-0">Introduction
to Linear Mixed Effects Models</a><br />
November 18-November 19, 2024 1:00-3:00pm PST</p>
<p><a href="https://gladstone.org/events/scatac-seq-and-scrna-seq-data-integration">scATAC-seq
and scRNA-seq Data Integration</a><br />
November 22, 2024 1:00-4:00pm PST</p>
<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
RNA-Seq Analysis Using R</a><br />
February 20, 2025 9:00am-12:00pm PST</p>
<ul>
<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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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"
subtitle: "Part 1"
author: "Natalie Elphick"
date: "November 11th, 2024"
date: "January 27th, 2025"
knit: (function(input, ...) {
rmarkdown::render(
input,
@ -27,8 +27,10 @@ knitr::opts_chunk$set(comment = "")
## Introductions
**Natalie Elphick**
Bioinformatician I
Bioinformatician II
**Michela Traglia**
Senior Statistician
@ -464,7 +466,7 @@ 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
- Intuitive syntax
- Comprehensive (data manipulation, cleaning, modeling and graphics)
@ -475,19 +477,18 @@ packages
# End of Part 1
## 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
[Introduction to scATAC-seq Data Analysis](https://gladstone.org/events/introduction-scatac-seq-data-analysis)
November 14 - November 15, 2024 1:00-4:00pm PST
[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 Linear Mixed Effects Models](https://gladstone.org/events/introduction-linear-mixed-effects-models-0)
November 18-November 19, 2024 1:00-3:00pm 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
[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
- 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"
subtitle: "Part 2"
author: "Natalie Elphick"
date: "November 12th, 2024"
date: "January 28th, 2025"
knit: (function(input, ...) {
rmarkdown::render(
input,
@ -29,7 +29,7 @@ knitr::opts_chunk$set(comment = "")
# Introductions
**Natalie Elphick**
Bioinformatician I
Bioinformatician II
**Min-Gyoung Shin**
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.
- 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)
- [.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
@ -301,21 +302,21 @@ Code templates can be used to avoid typing the same code over and over again.
# End of Part 2
## 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
[Introduction to scATAC-seq Data Analysis](https://gladstone.org/events/introduction-scatac-seq-data-analysis)
November 14 - November 15, 2024 1:00-4:00pm PST
[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 Linear Mixed Effects Models](https://gladstone.org/events/introduction-linear-mixed-effects-models-0)
November 18-November 19, 2024 1:00-3:00pm 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
[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
- 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-r-data-analysis.Rproj
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@ -1,4 +1,5 @@
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