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prabhakarlab / Banksy

BANKSY: spatial clustering
https://prabhakarlab.github.io/Banksy
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Multi-sample integration analysis #5

Closed hzongyao closed 2 years ago

hzongyao commented 2 years ago

I saw in your example data that the software can achieve simultaneous analysis of multiple samples and can identify the results of inter-sample consistency clustering（https://prabhakarlab.github.io/Banksy/articles/dlpfc-analysis.html）, I would like to ask if this result can be interpreted as the integrated analysis result after removing the potential batch effect between samples? Thank you!

vipulsinghal02 commented 2 years ago

Hi Hzongyao,

I think the best way to think about it is simply processing multiple datasets together. Once you have batch corrected (say by count normalizing, or using something fanceir like scTransfrom or even anchor based data integration tools), you can cluster all your datasets in one go with BANKSY, and that way cell types that appear in multiple datasets all get labeled as one cell type.

hzongyao commented 2 years ago

Thank you very much for your reply, I will read the article you recommended about the methodology of spatial correlation analysis, in short, thank you very much for the tool your team developed, it is a great job!

vipulsinghal02 commented 2 years ago

Absolutely, glad it can be useful for you!