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docs/Intro_to_R_data_analysis_part_2.html
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@ -2809,7 +2809,7 @@ border: 0;
<h1>Introductions</h1>
<p><strong>Natalie Elphick</strong><br />
Bioinformatician I</p>
<p><strong>Michela Traglia (In Person TA)</strong><br />
<p><strong>Michela Traglia (Online TA)</strong><br />
Senior Statistician</p>
<p><strong>Yihang Xin (Online TA)</strong><br />
Software Engineer III</p>
@ -2822,6 +2822,8 @@ Software Engineer 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>Where to get help</li>
</ol>
</section>
@ -3046,7 +3048,7 @@ 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_4ff84877" 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_c802e9da" 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>
@ -4586,6 +4588,38 @@ case</li>
</ul>
</section></section>
<section>
<section id="where-to-get-help" class="title-slide slide level1">
<h1>Where to Get Help</h1>
</section>
<section id="bioinformatics-questions" class="slide level2">
<h2>Bioinformatics Questions</h2>
<p>For any bioinformatics specific questions feel free to reach out to
the Gladstone Bioinformatics Core.</p>
<ul>
<li>Email
<ul>
<li><a href="mailto:bioinformatics@gladstone.ucsf.edu">bioinformatics@gladstone.ucsf.edu</a></li>
</ul></li>
<li>Slack channel #questions-about-bioinformatics
<ul>
<li>Contact us at the email above to be added to the channel</li>
</ul></li>
</ul>
</section>
<section id="debugging-errors" class="slide level2">
<h2>Debugging Errors</h2>
<ul>
<li>Try searching the web by pasting the error message and any relevant
keywords (package or function name)</li>
<li>Websites like <a href="https://stackoverflow.com/">Stack
Overflow</a> and <a href="https://forum.posit.co/">Posit Community
Forum</a> should have the most relevant answers</li>
<li>If the problem is package specific, check the documentation and
reach out to the authors using their preferred method</li>
</ul>
</section></section>
<section>
<section id="additional-resources" class="title-slide slide level1">
<h1>Additional Resources</h1>
@ -4593,15 +4627,14 @@ case</li>
<section id="r" class="slide level2">
<h2>R</h2>
<ul>
<li><p><a href="https://r4ds.hadley.nz/">R for Data Science</a></p></li>
<li><p><a href="https://statsandr.com/blog/top-10-errors-in-r/">Top 10 R
Errors and How to Fix them</a></p></li>
<li><p><a href="https://bookdown.org/yihui/rmarkdown/how-to-read-this-book.html">R
Markdown: The Definitive Guide</a> : Excellent R markdown
reference</p></li>
<li><p><a href="https://ggplot2-book.org/">ggplot2: elegant graphics for
data analysis</a></p></li>
<li><p><a href="https://adv-r.hadley.nz/">Advanced R</a></p></li>
<li><a href="https://r4ds.hadley.nz/">R for Data Science</a></li>
<li><a href="https://statsandr.com/blog/top-10-errors-in-r/">Top 10 R
Errors and How to Fix them</a></li>
<li><a href="https://bookdown.org/yihui/rmarkdown/how-to-read-this-book.html">R
Markdown: The Definitive Guide</a></li>
<li><a href="https://ggplot2-book.org/">ggplot2: elegant graphics for
data analysis</a></li>
<li><a href="https://adv-r.hadley.nz/">Advanced R</a></li>
</ul>
</section>
<section id="statistics" class="slide level2">
@ -4656,8 +4689,12 @@ can continue to improve these workshops</li>
<p><a href="https://gladstone.org/events/single-cell-atac-seq-data-analysis-part-2-1">Single
Cell ATAC-Seq Data Analysis Part 2</a></p>
<ul>
<li>Check <a href="https://gladstone.org/events?series=data-science-training-program">this
link</a> at the end of the summer for out fall workshop schedule</li>
<li><p>Check <a href="https://gladstone.org/events?series=data-science-training-program">this
link</a> at the end of the summer for out fall workshop
schedule</p></li>
<li><p><a href="https://github.com/gladstone-institutes/Bioinformatics-Workshops/wiki">Gladstone
Bioinformatics Workshops</a> - workshop wiki page for all of the
workshops we offer</p></li>
</ul>
</section></section>
</div>

33
intro-r-data-analysis/Intro_to_R_data_analysis_part_2.Rmd
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@ -31,7 +31,7 @@ knitr::opts_chunk$set(comment = "")
**Natalie Elphick**
Bioinformatician I
**Michela Traglia (In Person TA)**
**Michela Traglia (Online TA)**
Senior Statistician
**Yihang Xin (Online TA)**
@ -43,6 +43,9 @@ Software Engineer III
2. Filtering and reformatting data
3. Plotting data
4. Hands on data analysis
5. ChatGPT tips for R
6. Where to get help
# Introduction to Tidyverse
@ -227,7 +230,6 @@ read_xlsx("Intro_to_R_workshop_materials/PanTHERIA.xlsx") |>
- We will read in the data and explore if the trophic level has a significant impact on the adult body mass of mammals
Steps:
1. Combine and clean the data
2. Visualize adult body mass by trophic level
@ -260,18 +262,33 @@ Steps:
- Check out the file: `example_code/1_convert_syntax_example.R` for an example use case
# Where to Get Help
## Bioinformatics Questions
For any bioinformatics specific questions feel free to reach out to the Gladstone Bioinformatics Core.
- Email
- [bioinformatics@gladstone.ucsf.edu](mailto:bioinformatics@gladstone.ucsf.edu)
- Slack channel #questions-about-bioinformatics
- Contact us at the email above to be added to the channel
## Debugging Errors
- Try searching the web by pasting the error message and any relevant keywords (package or function name)
- Websites like [Stack Overflow](https://stackoverflow.com/) and [Posit Community Forum](https://forum.posit.co/) should have the most relevant answers
- If the problem is package specific, check the documentation and reach out to the authors using their preferred method
# Additional Resources
## R
- [R for Data Science](https://r4ds.hadley.nz/)
- [Top 10 R Errors and How to Fix them](https://statsandr.com/blog/top-10-errors-in-r/)
- [R Markdown: The Definitive Guide](https://bookdown.org/yihui/rmarkdown/how-to-read-this-book.html) : Excellent R markdown reference
- [R Markdown: The Definitive Guide](https://bookdown.org/yihui/rmarkdown/how-to-read-this-book.html)
- [ggplot2: elegant graphics for data analysis](https://ggplot2-book.org/)
- [Advanced R](https://adv-r.hadley.nz/)
## Statistics
- [Data Analysis in R](https://bookdown.org/steve_midway/DAR) : This book has more statistics details than *R for Data Science*
@ -300,7 +317,9 @@ Steps:
[Single Cell ATAC-Seq Data Analysis Part 2](https://gladstone.org/events/single-cell-atac-seq-data-analysis-part-2-1)
- Check [this link](https://gladstone.org/events?series=data-science-training-program) at the end of the summer for out fall workshop schedule
- Check [this link](https://gladstone.org/events?series=data-science-training-program) at the end of the summer for out fall workshop schedule
- [Gladstone Bioinformatics Workshops](https://github.com/gladstone-institutes/Bioinformatics-Workshops/wiki) - workshop wiki page for all of the workshops we offer