# New basic scanpy tutorial

## Topics

* Doublet detection
* Filtering
* MAD
* After an initial clustering – e.g. look for qc problems first
*
* Doublet detection
* How to recommend for annotation
* Use some sort of automation for this process
* Grab
* Figshare for dataset
* Multiome
* Cite-seq
* Subset data to reasonable size
* Figure out where to host

## Resources

* Best practices annotation chapter: https://app.reviewnb.com/theislab/cross-modal-single-cell-best-practices/pull/85/
* Includes marker genes
* Raw data: https://drive.google.com/drive/folders/1LfoMoVndY9ioORZ45O0egoC9_HUpLsHQ?usp=sharing

## Tasks

- [ ] Preprocessing (Anna)
- [ ] Doublet detection
- [ ] Annotation (Daniel)
- [ ] Viz (Karin)