Welcome to the Course!

Getting Ready for Your First Day!

Author

Affiliation

Lindsay Hayes

Department of Cell Biology, OUHSC

Pre-lecture activities

The course will exclusively use R in the integrated development environment (IDE) called R Studio. Since the summer semester is only 1 month (10 classes), it is critical to have your computer set up and ready to go before the first day of class.

Throughout the course, there will be a set of pre-lecture activities and/or readings for you to complete. These activities prepare you for the in-class activities. Failure to complete them will put you behind in an already compressed course.

To prepare for the first class:

1. Install R and R Studio
   • installation video tutorial
   • Detailed instructions on installing R and R Studio are available on swirl.
     • Complete step 1 and step 2

Tip

Swirl is a great tool to learn R interactively that we will use in the course. Feel free to explore more.

2. In the first class, we will begin to get familiar with R. Complete the Pre-reading material about R. Pre-reading materials for each class are located under Resources. Sometimes, pre-reading materials are direct links to external resources for you to read in advance of the lecture.

Lecture

Learning objectives

Learning objectives

At the end of this lesson you will:

• Get an overview of the course (including staff, format, grading, etc)
• Be able to recognize and operate an Integrated Developer Environment (IDE).
• Be able to recognize a Quarto document and describe reasons why to use a unified authoring framework.
• Be able to create a R project & Quarto document.

Slides

• Lecture 01: Welcome and Introductions

• In-Class Activity

Acknowledgements

Material for this lecture was borrowed and adopted from

• sw carpentry: https://carpentries-incubator.github.io/bioc-intro/20-r-rstudio.html
• data carpentry: https://datacarpentry.github.io/genomics-r-intro/00-introduction.html

Post-lecture Practice

Summary

• Access all course material on the course website (https://lindsaynhayes.github.io/introR2025/).
• RStudio makes you a more efficient programmer and gives you easy access to all the components of data analysis.
• Quarto is an open-source scientific and technical publishing system to create reproducible, production quality data analysis reports and much more. During the course we will primarily use the HTML output format.

Additional practice

Here are some additional practice questions to help you think about the material discussed.

Check out this article on the 10 Best Practices for Data Science here

Practice Tasks

1. In RStudio, create a new R project and then create a new Quarto document in that R project. Read the instructions. Practice running the chunks individually using the “play” button and the keyboard short cut.

2. Change the settings of the Quarto document to display the output “inline” or in the “console”.

3. Render the document and view the HTML output. Verify that you can modify the code, re-run it, and see modified output.