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August 2024 updates
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Natalie Elphick
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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: "May 20th, 2024"
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date: "August 26th, 2024"
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knit: (function(input, ...) {
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rmarkdown::render(
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input,
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@ -29,8 +29,8 @@ knitr::opts_chunk$set(comment = "")
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**Natalie Elphick**
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Bioinformatician I
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**Yihang Xin (Online TA)**
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Software Engineer III
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**Min-Gyoung Shin**
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Bioinformatician III
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## Poll 1
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@ -47,6 +47,24 @@ Software Engineer III
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- No background in statistics or computing
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- No prior experience with programming or R/RStudio
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## Learning Objectives
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1. Navigate the RStudio environment and understand how R works
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2. Understand variable types and data structures
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3. Perform data cleaning and transformation in R
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4. Create simple visualizations using ggplot2
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## Learning R Takes Time!
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- **Workshop Pace**: This is an intro, and it’s okay if everything doesn’t click right away.
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- **Practice is Key**: Plan to spend extra time on practicing concepts after the workshop.
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- **Self-Guided Learning**: Use the materials provided at the end of the workshop to continue at your own pace.
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Keep at it—progress comes with persistence!
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## Part 1:
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1. What is R and why should you use it?
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- Can easily implement any statistical analysis
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- Code serves as a record which enables reproducibility
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with minimal effort
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- As of March 2023, there were over 19,000 open source packages to extend its
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- As of August 2024, there were over 21,000 open source packages to extend its
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functionality
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- Highly customizable graphics ([ggplot2](https://ggplot2-book.org/))
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- Analysis reports ([knitr](https://cran.r-project.org/web/packages/knitr/index.html))
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- RNA-seq analysis ([DESeq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html))
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## How does it work?
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<section class="shrink">
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</section>
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# RStudio
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## RStudio
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- RStudio is an integrated development
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environment (IDE)
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- It is an app that makes R code easier to write by providing a
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feature rich graphical user interface (GUI)
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- An app that makes R code easier to write by providing a feature rich graphical user interface (GUI)
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<br>
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</br>
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@ -109,7 +122,7 @@ feature rich graphical user interface (GUI)
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## File types
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- **Rscript** files that end in `.R`
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- The most basic, a file that contains R code
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- The most basic, a file that contains only R code
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- **RMarkdown** files that end in `.Rmd`
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- Let's create a blank Rscript to see how they work, open RStudio and click:
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- File -\> New File -\> R Script
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@ -228,7 +241,7 @@ DogBreeds <- c("Labrador Retriever", "Akita", "Bulldog")
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## Data Types
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- Integer
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- Whole numbers (in R denoted with L ex. 1L,2L)
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- Whole numbers (denoted with L ex. 1L,2L)
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- Numeric
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- Decimal numbers
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- Logical
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@ -312,7 +325,7 @@ x %in% y # Is x in this vector y?
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**What is the output of the following code?**
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```{r, eval = FALSE}
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4 %in% as.character(c(1,2,3,4))
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4 %in% c(1, 2, 3, 4)
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```
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1. TRUE
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@ -352,10 +365,15 @@ execution of code
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```{r}
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dog_breeds <- c("Labrador Retriever", "Akita", "Bulldog")
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if ("Akita" %in% dog_breeds) {
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print("dog_breeds already contains Akita")
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} else {
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dog_breeds <- c("Akita", dog_breeds)
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}
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```
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@ -372,13 +390,12 @@ perform a single action
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## Defining a function
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- To define a function we use the function keyword, the output is specified with the **return** keyword:
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- To define a function we use the function keyword, the output is specified with the **return** function:
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```{r}
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add_dog <- function(dog_to_add,
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input_vector) {
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add_dog <- function(dog_to_add, input_vector) {
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if (dog_to_add %in% input_vector) {
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message("Already contains this dog")
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print("Already contains this dog")
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} else {
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@ -453,8 +470,16 @@ packages
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## Upcoming Workshops
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[Single Cell ATAC-Seq Data Analysis Part 2](https://gladstone.org/events/single-cell-atac-seq-data-analysis-part-2-1)
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[Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-5)
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September 10, 2024 9am-12pm PDT
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- Check [this link](https://gladstone.org/events?series=data-science-training-program) at the end of the summer for out fall workshop schedule
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[Introduction to Statistics, Experimental Design, and Hypothesis Testing](https://gladstone.org/events/introduction-statistics-experimental-design-and-hypothesis-testing-1)
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September 10 - September 12, 2024 1-3pm PDT
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[Single Cell RNA-Seq Data Analysis](https://gladstone.org/events/single-cell-rna-seq-data-analysis-0)
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September 16-September 17, 2024 9am-4pm 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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@ -2,7 +2,7 @@
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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: "May 21st, 2024"
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date: "August 27th, 2024"
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knit: (function(input, ...) {
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rmarkdown::render(
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input,
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@ -31,11 +31,11 @@ knitr::opts_chunk$set(comment = "")
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**Natalie Elphick**
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Bioinformatician I
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**Michela Traglia (Online TA)**
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**Michela Traglia**
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Senior Statistician
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**Yihang Xin (Online TA)**
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Software Engineer III
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**Ayushi Agrawal**
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Bioinformatician III
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# Schedule
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@ -179,7 +179,7 @@ ggplot(data = mpg, # Input dataframe
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```{r, fig.dim=c(10,4)}
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ggplot(data = mpg,
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mapping = aes(x = cty, y = hwy)) +
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geom_point() +
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geom_point(color = "brown") +
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geom_smooth(formula = y ~ x, method = "lm")
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```
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@ -315,11 +315,17 @@ For any bioinformatics specific questions feel free to reach out to the Gladston
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## Upcoming Workshops
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[Single Cell ATAC-Seq Data Analysis Part 2](https://gladstone.org/events/single-cell-atac-seq-data-analysis-part-2-1)
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[Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-5)
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September 10, 2024 9am-12pm PDT
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- Check [this link](https://gladstone.org/events?series=data-science-training-program) at the end of the summer for out fall workshop schedule
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[Introduction to Statistics, Experimental Design, and Hypothesis Testing](https://gladstone.org/events/introduction-statistics-experimental-design-and-hypothesis-testing-1)
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September 10 - September 12, 2024 1-3pm PDT
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- [Gladstone Bioinformatics Workshops](https://github.com/gladstone-institutes/Bioinformatics-Workshops/wiki) - workshop wiki page for all of the workshops we offer
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[Single Cell RNA-Seq Data Analysis](https://gladstone.org/events/single-cell-rna-seq-data-analysis-0)
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September 16-September 17, 2024 9am-4pm 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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/* Add horizontal scrolling to all code outputs */
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.reveal pre code.output {
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/* Bold slide titles and change color */
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.reveal h2 {
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font-weight: bold !important;
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color: #9c0366;
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color: #0072B2;
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}
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/* Bold slide titles and change color */
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.reveal h1 {
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font-weight: bold !important;
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color: #9c0366;
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color: #0072B2;
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}
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.reveal .slides>section:first-child h2 {
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color: #333;
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/* Custom slide title */
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.my-title-slide h1 {
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font-weight: bold;
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color: #9c0366;
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color: #0072B2;
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}
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.my-title-slide h2 {
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color: #333;
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.reveal .slides>section:first-child h1 {
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font-weight: bold !important;
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color: #9c0366;
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color: #0072B2;
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}
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/* Increase the spacing between list items */
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color: #0c74dc;
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}
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/* Change link color to magenta on hover */
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/* Change link color to darker blue on hover */
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.reveal a:hover {
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color: #9c0366 !important;
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color: #0072B2 !important;
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}
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