Upcoming Workshops
-Introduction
-to Unix Command Line
-February 10-February 11, 2025 1:00-3:00pm PST
-Introduction
-to RNA-Seq Analysis
-February 13-February 14, 2025 1:00-4:00pm PST
-Intermediate
+Introduction
+to RNA-Seq
+May 12-May 13, 2025 1:00-4:00pm PDT
+Intermediate
RNA-Seq Analysis Using R
-February 20, 2025 9:00am-12:00pm PST
+May 19, 2025 1:00-4:00pm PDT
- Check this
link at for the full schedule
diff --git a/intro-r-data-analysis/Intro_to_R_data_analysis_part_1.Rmd b/intro-r-data-analysis/Intro_to_R_data_analysis_part_1.Rmd
index d433254..3337184 100644
--- a/intro-r-data-analysis/Intro_to_R_data_analysis_part_1.Rmd
+++ b/intro-r-data-analysis/Intro_to_R_data_analysis_part_1.Rmd
@@ -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
diff --git a/intro-r-data-analysis/Intro_to_R_data_analysis_part_2.Rmd b/intro-r-data-analysis/Intro_to_R_data_analysis_part_2.Rmd
index 9c0ebe4..b914f00 100644
--- a/intro-r-data-analysis/Intro_to_R_data_analysis_part_2.Rmd
+++ b/intro-r-data-analysis/Intro_to_R_data_analysis_part_2.Rmd
@@ -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 = "")
*Press the ? key for tips on navigating these slides*
# 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