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hkim240 / CellNeighborEX

CellNeighborEX: Deciphering Neighbor-Dependent Gene Expression from Spatial Transcriptomics Data
MIT License
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multiple sample #2

Open SGIlabes opened 2 months ago

SGIlabes commented 2 months ago

Your package idea seems very good. Is it possible to apply it to multiple samples as well? In my data, each sample has its own local x and y coordinates. And I have a merged object.

hkim240 commented 2 months ago

Thank you for your interest. It is possible to apply CellNeighborEX to spatial transcriptomics data with multiple samples. Since CellNeighborEX uses nearest neighbors to identify cell contact-dependent genes, I recommend running it for each sample individually. If necessary, after correcting batch effects among the multiple samples, you can provide the corrected transcriptome profiles as input.