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Add Seurat Integration into SnapATAC2 #339

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@beyondpie beyondpie commented Sep 11, 2024

Hi Kai,

Currently, I am testing AllCool's Seurat integration. I find that it can be easily extracted from AllCool's package.

I create this PR to record this, and I am still testing their scripts and updating the documents. So it may take some time still.

Currently, the scripts need lots of documents and also we need to add their license (maybe in the submodule).

Please ignore the peak calling part. I will remove them in the future.
Thanks!
Songpeng

@beyondpie beyondpie self-assigned this Sep 11, 2024
@beyondpie beyondpie added the enhancement ✨ New feature or request label Sep 11, 2024
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beyondpie commented Sep 25, 2024

I've tested the codes. In general, it works for scipy AnnData. I think for the use of SnapATAC2, we simply need to load the object into memory.

In the future, if we want, we can adapt the SnapATAC2's dimension reduction to this module.

I plan to add more documentations for the module, and then maybe you can consider to put it wherever you want (probably snapatac2-contrib, since it's not that mature.) No pressure, you are the boss.

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