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 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.