Hello! This repository contains the resources I used for my "R for cytometry course." You are welcome to learn and teach using this material, please just credit me if you reproduce any of it.
- Install R for your operating system from here: https://cran.r-project.org/
- Install Rstudio for your operating system here: https://posit.co/download/rstudio-desktop/
- Download the contents of this repository to your computer. The easiest way to do this is to click Code then Download ZIP as shown below
- Unzip the folder somewhere sensible on your computer
- Open each of the html files in the folder and code along in Rstudio yourself! If you are new to R, I recommend starting with Intro-to-R-and-RStudio.html, followed by Plotting-data-with-ggplot2.html. For cytometry-specific content, follow along with High-dimensional-analysis-with-Spectre.html and Manual-flow-cytometry-analysis-with-R.html. I would suggest creating a separate Rstudio project for each tutorial, and copying the data folder that you unzipped, into the project folder so you have the relevant data for each tutorial.
I also made a short example on using the CytoExploreR package for interactive point and click gating in R, but haven't turned this into a html tutorial yet. This isn't everything, in particular, I haven't touched upon the openCyto package for automated gating, but I have materials on this if you'd like to learn more.
If you have questions, you can reach me at [email protected] and I'll try my best to help.
Check out the homework folder that you unzipped! There are some practice questions in there. Otherwise, the best way to learn is to struggle through analysing your own data using these materials. Focus on doing, not memorising.