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massonix / HCATonsilData

Provide programmatic access to the tonsil cell atlas datasets
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Advise on how to merge two subsetted CITE-seq objects from the tonsil CITE-seq Seurat object? #13

Open denvercal1234GitHub opened 1 year ago

denvercal1234GitHub commented 1 year ago

Hi there,

Thanks again for all of your help in leveraging the great dataset you generated.

I subsetted the whole tonsil cite-seq Seurat object to obtain 2 cite-seq objects (one object for B cells expressing CD38 and one object for B cells not expressing CD38).

I followed the codes you kindly deposited to perform WNN analysis of RNA+ADT for each of these 2 objects, including harmony to integrate by "gem_ID" within each object within each object.

I now hope to merge these 2 B cell objects and cluster them using RNA+ADT.

Would you minding providing some opinion whether I should simply use merge() or what is the recommended workflow?

Thank you very much!