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navinlabcode / copykat

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Scanpy Support #24

Closed mbcouger closed 2 years ago

mbcouger commented 3 years ago

Hello,

Really like the paper, is there protocol or method for using this with the scanpy platform?

Cheers, Brian

gaobio commented 3 years ago

Hello,

Really like the paper, is there protocol or method for using this with the scanpy platform?

Cheers, Brian

Thanks Brian. CopyKAT can directly take the UMI count matrix as input. It should work with scanpy or seurat as long as you pull out the count matrix from these objects.

grst commented 2 years ago

fyi, we now provide a wrapper for copykat as part of the infercnvpy package that works directly with scanpy objects. More details here: infercnvpy.tl.copykat.

gaobio commented 2 years ago

fyi, we now provide a wrapper for copykat as part of the infercnvpy package that works directly with scanpy objects. More details here: infercnvpy.tl.copykat.

that's cool. Please notice that copykat is updated and mouse data is now supported

grst commented 2 years ago

Please notice that copykat is updated and mouse data is now supported

Currently we just make a call to your R package, I don't see any reason why it wouldn't work with the updated version. A true python-version would be a lot cooler though (#46), managing the R dependencies from Python can be quite painful.