An Introduction to R for RNA-Seq Analysis¶
RNA-Sequencing (RNA-Seq) is a popular method for determining the presence and quantity of RNA in biological samples. In this 3 hour workshop, we will use R to explore publicly-available RNA-Seq data from the Gene Expression Tissue Project (GTEx). Attendees will be introduced to the R syntax, variables, functions, packages, and data structures common to RNA-Seq projects. We will use RStudio to import, tidy, transform, and visualize RNA-Seq count data. Attendees will learn tips and tricks for making the processes of data wrangling and data harmonization more manageable. This workshop will not cover cloud-based workflows for processing RNA-seq reads or statistics and modeling because these topics are covered in our RNA-Seq Concepts and RNA-Seq in the Cloud workshops. Rather, this workshop will focus on general R concepts applied to RNA-Seq data.
| Est. Time | Lesson name | Description |
|---|---|---|
| 25 min | Introduction | Overview of RStudio and Binder |
| 30 min | Import Data | Importing data with read.csv and read.table |
| 30 min | Visualize Data | Visualizing data with ggplot2 |
| 90 min | Wrangle Data | Tyding and transforming data |
| 5 min | Wrap-up | Resources |
Learning Objectives¶
In this workshop, you will learn how to use R and RStudio to:
- import and view files commonly associated with RNA-sequencing experiments
- select variables and observations that are relevant to research questions (tidy)
- create and rename variables (transform)
- join data frames by common variables (harmonize)
- visualize data using bar graphs, scatter plots, and box plots
Please refer to the RStudio cheat sheets for commonly used R functions. The R for Data Science book provides in depth descriptions and examples of many functions and concepts covered in this course.
Here are the notes from workshops taught with these materials.
- May 11, 2022 workshop notes
- April 27, 2022 workshop notes
- March 23, 2022 workshop notes
Here is a 3 hours video of this workshop being taught at the May 2022 Hackathon.
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Familiarity with R and RNA Sequencing is not required but would be useful. This lesson uses a standardized binder environment, which will work on Windows, Mac, and Linux operating systems, and Firefox, Safari, and Chrome web browsers.