Comments (1)
huBioinfo
commented on July 1, 2024
Hi Jun,
I'm very sorry for replying late. Yes, CytoCommunity can be used for spot-based spatial omics like 10x visium data, but needs an additional procedure, that is, cell-type deconvolution. First, you can apply cell-type deconvolution methods (e.g. CARD, by Ma Y, Nature Biotechnology, 2022) to 10x visium data (usually single-cell transcriptomics data as reference) to obtain cell type fractions for each spot. Then, you can construct a spot-spot proximity graph and use the cell type fraction as the attribute vector of each spot. So the Step1.py should be revised since there will be no CellTypeLabel.txt. If you need further assistance on how to revise the code in Step1.py, please contact me via email: [email protected]
Best,
Yuxuan
from cytocommunity.
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