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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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a question about data formats #308

Open rachel662 opened 2 years ago

rachel662 commented 2 years ago

Hi there I would like to use 2 available scRNA-seq datasets and use cellchat to infer cell-cell communication between cell types for one of the publically available datasets I am only interested in 2 of the clusters they identified I have a merged seurat object of the dataset and seurat objects of each dataset separately too

is it possible to run cellchat with each of the two clusters of the dataset i mention previously separately so I can see how these cell types might interact differently with the cell types in the other dataset? and if so, would you have any advice on how to go about doing it?

cheers Rachel

sqjin commented 2 years ago

@rachel662 Yes, you can run cellchat seperately on each dataset and then use the mergeCellChat function to perform comparison analysis

rachel662 commented 2 years ago

Hi there, thanks so much for your time, really appreciate it would my workflow go something like this? subset out each of the 2 clusters I am interested in from one dataset individually and make a cellchat object with each of them make a cellchat object of the other dataset merge this cellchat object with the 2 I have made from the other dataset separately continue with the analysis to compare the two?

thanks again for your help, I really appreciate it Cheers Rachel