This is a collection of resources for learning the basics of scRNA-seq analysis. I wrote these scripts during spring 2024 and used them to train younger undergraduates who would be taking over for me in the Grainger Lab at the University of Virginia upon my graduation.
Day 1: Seurat Workflow Part 1 -- Setting up the object and the basic process
Day 2: Seurat Workflow Part 2 -- Adding QC and finishing the process
Day 3: Packages and Package Managers
Day 4: What happens if you run out of RAM? -- Our workstation and Rivanna
Day 5: Differential Expression Analysis
Day 6: Practice Assignment
Day 7: Other Useful Things
Day 8: Where does the data actually come from? -- Aligning reads and counting them
I have made the OneDrive folder that holds all of the example data public.
File paths will have to be altered accordingly if you use these scripts.
This repository is no longer updated. Furthermore, this repository does not represent the actual workflow that I use for scRNA-seq data analysis, nor does it represent my current understanding of the methods covered. This repository serves as a record of my creating and teaching this unofficial course during a weekly lab meeting.