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update for May 2025
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Natalie Elphick
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---
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title: "Introduction to R Data Analysis"
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subtitle: "Part 1"
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author: "Natalie Elphick"
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date: "January 27th, 2025"
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author: "Natalie Gill"
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date: "May 5th, 2025"
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knit: (function(input, ...) {
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rmarkdown::render(
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input,
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@ -26,13 +26,9 @@ knitr::opts_chunk$set(comment = "")
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## Introductions
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**Natalie Elphick**
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**Natalie Gill**
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Bioinformatician II
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**Michela Traglia**
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Senior Statistician
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## Poll 1
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@ -83,7 +79,7 @@ Keep at it—progress comes with persistence!
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## R
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- An open source language developed for statistical computing by **R**oss Ihaka and **R**obert Gentleman
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- Inspired by the **S** language developed at Bell labs in 1976 to make interactive data analysis easier
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- Developed at Bell labs in 1976 to make interactive data analysis easier
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- The first official version was released in 2000
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## Why use R for data analysis?
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@ -266,7 +262,7 @@ NA + 1
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1. "1.5" - Numeric
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2. "A" - Character
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3. 1L - Integer
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4. TRUE - Boolean
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4. TRUE - Boolean/Logical
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@ -466,7 +462,7 @@ packages
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## Why use Tidyverse Packages?
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- Most of the work in data analysis is getting data into the correct format to create outputs (plots and tables)
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- Much of the work in data analysis is getting data into the correct format to create outputs (plots and tables)
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- The tidyverse collection of packages simplifies this process
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- Intuitive syntax
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- Comprehensive (data manipulation, cleaning, modeling and graphics)
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@ -476,19 +472,30 @@ packages
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# End of Part 1
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## Schedule for Part 2
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1. Introduction to Tidyverse
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2. Filtering and reformatting data
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3. Plotting data
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4. Hands on data analysis
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5. AI tips for R
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6. Where to get help
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## Workshop survey
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- Please fill out our [workshop survey](https://www.surveymonkey.com/r/bioinfo-training) so we can continue to improve these workshops
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## Upcoming Workshops
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[Introduction to Unix Command Line](https://gladstone.org/events/introduction-unix-command-line-2)
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February 10-February 11, 2025 1:00-3:00pm PST
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[Introduction to RNA-Seq](https://gladstone.org/events/introduction-rna-seq-0)
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May 12-May 13, 2025 1:00-4:00pm PDT
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[Introduction to RNA-Seq Analysis](https://gladstone.org/events/introduction-rna-seq-analysis-8)
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February 13-February 14, 2025 1:00-4:00pm PST
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[Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-6)
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February 20, 2025 9:00am-12:00pm PST
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[Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-7)
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May 19, 2025 1:00-4:00pm PDT
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- Check [this link](https://gladstone.org/events?series=data-science-training-program) at for the full schedule
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---
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title: "Introduction to R Data Analysis"
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subtitle: "Part 2"
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author: "Natalie Elphick"
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date: "January 28th, 2025"
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author: "Natalie Gill"
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date: "May 6th, 2025"
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knit: (function(input, ...) {
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rmarkdown::render(
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input,
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@ -28,11 +28,9 @@ knitr::opts_chunk$set(comment = "")
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<center>*Press the ? key for tips on navigating these slides*</center>
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# Introductions
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**Natalie Elphick**
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**Natalie Gill**
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Bioinformatician II
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**Min-Gyoung Shin**
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Bioinformatician III
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# Schedule
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@ -40,7 +38,7 @@ Bioinformatician III
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2. Filtering and reformatting data
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3. Plotting data
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4. Hands on data analysis
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5. ChatGPT tips for R
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5. AI tips for R
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6. Where to get help
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@ -239,12 +237,13 @@ Steps:
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# ChatGPT Tips for R
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# AI Tips for R
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## General Tips
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- Follow any relevant institutional guidelines on using LLMs
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- Always confirm ChatGPT's outputs are correct
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- Always confirm the outputs are correct
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- Provide as much detail as possible about the problem in the 1st prompt
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- Use separate chats for separate tasks/projects
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- Try the 'Custom Instructions' function
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@ -253,7 +252,7 @@ Steps:
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- Commented R code yields better responses
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- Provide the code and error message in the same prompt
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- ChatGPT can work well to convert syntax and improve your code:
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- LLMs can work well to convert syntax and improve your code:
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- "Turn this loop into a function : [your code]"
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- "Is there a better way to do this : [your code]"
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- Check out the file: `example_code/1_convert_syntax_example.R` for an example use case
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@ -306,14 +305,12 @@ Code templates can be used to avoid typing the same code over and over again.
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## Upcoming Workshops
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[Introduction to Unix Command Line](https://gladstone.org/events/introduction-unix-command-line-2)
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February 10-February 11, 2025 1:00-3:00pm PST
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[Introduction to RNA-Seq](https://gladstone.org/events/introduction-rna-seq-0)
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May 12-May 13, 2025 1:00-4:00pm PDT
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[Introduction to RNA-Seq Analysis](https://gladstone.org/events/introduction-rna-seq-analysis-8)
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February 13-February 14, 2025 1:00-4:00pm PST
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[Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-7)
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May 19, 2025 1:00-4:00pm PDT
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[Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-6)
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February 20, 2025 9:00am-12:00pm PST
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- Check [this link](https://gladstone.org/events?series=data-science-training-program) at for the full schedule
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