Question

scRNA-seq python tutorial

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5.1 years ago

brc ▴ 30

I'm looking for a python tutorial on scRNA-seq/RNS-seq data analysis. It will be helpful if someone could point towards the relevant resources.

scRNA-seq python RNA-seq • 7.7k views

ADD COMMENT • link updated 13 months ago by Ram 43k • written 5.1 years ago by brc ▴ 30

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Here is a nice compilation of all things scRNA by @Sean Davis: https://github.com/seandavi/awesome-single-cell While mostly R there are some Python things in there.

ADD REPLY • link 5.1 years ago by GenoMax 141k

score 6 · Answer 1 · 2019-03-13

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5.1 years ago

Friederike 8.9k

The scanpy tutorials might be a good start.

ADD COMMENT • link 5.1 years ago by Friederike 8.9k

score 5 · Answer 2 · 2019-07-30

Fabian Theis' lab has recently published Lücken & Theis, Current best practices in single‐cell RNA‐seq analysis: a tutorial together with a nice github repository in which you can find an example case study Jupyter notebook written in Python. I can highly recommend this.

In case you would like to use it on your own data, you could head over to FASTGenomics. It is an online platform for single cell analytics and it offers a generalized version of the case study notebook, which might be applicable to your own dataset.