How to learn Scanpy

Question

[godwin]

What is the best resource on learning how to use scanpy for single cell RNA-Seq analysis?

[rpolicastro]

The scanpy vignettes themselves are actually pretty good. Just walk through them and the example analyses and they will cover most of the important processing concepts.

Answer 1

[Istvan Albert]

Specifically there is a separate web resource called ScanPy Tutorials here:

https://scanpy.readthedocs.io/en/stable/tutorials.html

You can install scanpy and run those tutorials via Google Colab, for example here is a tutorial I am currently developing myself

https://colab.research.google.com/drive/1EwxeDMQ2I3BXPE4h7qRSMju6PFEpLab7?usp=sharing

[godwin]

Thank you. I've checked out your tutorial. It is very explanatory. You stopped at principal component analysis though, so I would check back on it in a month's time. Do you know if it would have been completed by then?

[Istvan Albert]

went on vacation, I plan to continue it once I am back

Answer 2

[Prakki Rama]

You can take a look at this best practices online resource from Fabian Theis lab.