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scverse / anndata-tutorials

Use cases for anndata.
BSD 3-Clause "New" or "Revised" License
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Update getting-started with Adam's blog post #10

Closed falexwolf closed 2 years ago

falexwolf commented 2 years ago

Integrate https://adamgayoso.com/posts/ten_min_to_adata/ into the getting-started tutorial.

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falexwolf commented 2 years ago

@adamgayoso, could you check whether everything is correct?

https://icb-anndata-tutorials--10.com.readthedocs.build/en/10/getting-started.html

ivirshup commented 2 years ago

Should this just go in the main docs as it's more of an explanation?

ivirshup commented 2 years ago

We could also put that off until we've got a better notebook rendering system set up

falexwolf commented 2 years ago

If you're not seeing problems with the content, I don't see any reason to wait with merging if Adam would also be fine with how his material got integrated.

It's just an improvement to the main getting-started tutorial that's already linked on the main docs: https://anndata.readthedocs.io/en/latest/tutorials.html

I think it addresses Malte's years-long request for a 5 min-to-anndata tutorial at least to some degree.

But @LuckyMD will be the better person to make that call! ☺️

ivirshup commented 2 years ago

I've cut down on the notes at the top a bit.

I felt like they were getting into the weeds on topics which aren't critical to a very quick introduction to anndata. They could maybe come back as footnotes, but I don't think they were appropriate for emphasized text.

LuckyMD commented 2 years ago

I love this blog post! Awesome that's something like this is finally in the tutorials!

I haven't checked the jupyter notebook, but I think there was something about subsetting .obs by booleans or based on other .obs covariates that had some quirks, no? Also, if you could add sth like .groupby calls on .obs that would be quite nice.

Also, maybe some information on .rename_categories and the effects thereof would be useful (changing stored rank_genes_groups outputs).