CellChat and Visium (spatial transcriptomics)

[s849]

Hi,

I have some visium data sets on which I would like to try CellChat. Is it possible for CellChat to do this?

[sqjin]

@s849 I think you can infer the cell-cell communication using cellchat based on the gene expression and then can filter out the interactions if the two interacting cell types are spatially distant. There are several existing methods can help you to determine whether two cell types are co-localized. Here is one example study applying CellChat to spatial transcrimptomics ( https://www.biorxiv.org/content/10.1101/2021.11.24.469915v1 )

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