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sqjin / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
GNU General Public License v3.0
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CellChat and Visium (spatial transcriptomics) #335

Open s849 opened 2 years ago

s849 commented 2 years ago

Hi,

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

sqjin commented 2 years ago

@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 )

On Fri, Dec 3, 2021 at 5:43 AM s849 @.***> wrote:

Hi,

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

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