Single-cell is a rapid and exciting evolving field with numerous resources and classes/slides scattered online.
The idea of this repository is to act as a tentative curriculum that encompasses different areas where single-cell can serve as an important tool for scientific discovery. Serving as a quick-start guide to those starting.
The intention is not to collect every single tutorial in existence but aggregate the best resources that can give a comprehensive overview of the field.
PRs are extremely welcomed, together we can make a comprehensive and dynamic evolving curriculum for single-cell.
This repository would not exist if not for the awesome people that make their materials publicly available. I tried my best to give credits to authors of the tutorials/videos/slides, if you find anything incorrectly or would like to have it removed from this repository please let me know and it’ll be quickly fixed.
Some of the fields haven’t yet developed dedicated workshops/classes so they will be presented as tutorials of specific tools that are available.
This repository was largely inspired by awesome initiatives such as OSSU and Awesome Single-Cell, go check them out.
| Topic | Author | References |
|---|---|---|
| R for Data Science | Garrett Grolemund & Hadley Wickham | |
| Ggplot2 | Thomas Lin Pedersen |
scRNA is the most extensive documented area with a plethora of tutorials.
| Link | Authors | Publication |
|---|---|---|
| Orchestrating Single-Cell Analysis | Bioconductor | Reference |
| Topic | Author | References |
|---|---|---|
| Pre-Processing | ||
| Normalization | ||
| Feature Selection | ||
| Dimensionality Reduction | ||
| Clustering | ||
| Cell Annotation | ||
| Pseudotime | ||
| RNA Velocity |
Seurat
| Topic | Author | References |
|---|---|---|
| QC - Dimensional Reduction - Clustering - DE | Satija lab | 1 |
Scanpy
| Topic | Author | References |
|---|---|---|
| QC - Dimensional Reduction - Clustering - Marker genes | Alex Wolf, Fidel Ramirez, Sergei Rybakov |
Reading
| Topic | Authors | Publication |
|---|---|---|
| Integrative single-cell analysis | Tim Stuart & Rahul Satija | doi: 10.1038/s41576-019-0093-7 |