One tutorial that walks through a complete single-cell RNA-seq analysis in R, one step at a time, and explains why each step is there.
Just want to read it? Open the finished tutorial in your browser. All the code, plots and results are there, and you don't need to install anything.
Want to run it yourself?
Go to the beginner folder and follow the steps. It runs on a normal laptop, and you don't need any experience.
| Folder | What it is | Who it's for |
|---|---|---|
beginner/ |
Complete analysis of blood cells from 8 people, untreated vs treated with interferon. Runs on a laptop. | Anyone new to single-cell |
advanced/ |
Kidney single-nucleus data, starting from raw sequencing files on a computing cluster. Work in progress. | People with cluster access |
Code is MIT licensed (see LICENSE). The data belongs to the original authors: Kang et al. 2018 (beginner) and Wilson et al. 2019, GSE131882 (advanced). Please cite them if you use it.