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jinworks / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
GNU General Public License v3.0
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if scATAC data can use cellchat? #124

Open zhang-HZAU opened 1 month ago

zhang-HZAU commented 1 month ago

The cellchat tool is very useful, thank you for your team's contribution.

Now I want to try to perform cell communication analysis on scATAC data. Because no tools developed for scATAC have been found. I plan to use the activate gene matrix obtained by scATAC to perform the same operation as in cell communication in scRNA.

But I'm not sure if this is reasonable. I found it mentioned in the cellchat v1 readme: "In addition to infer the intercellular communication from any given single-cell data, CellChat provides functionality for further data exploration, analysis, and visualization." I think scATAC is single-cell data, but By v2, the description became "In addition to infer the intercellular communication from any given scRNA-seq and ...". Is the cellchat developed by your team not applicable to scATAC data?

Any suggestions on scATAC for cell communication are needed, thank you~

sqjin commented 1 month ago

@zhang-HZAU I think you take the gene activity as input of CellChat, and make sure the input data are non-negative.

zhang-HZAU commented 1 month ago

@zhang-HZAU I think you take the gene activity as input of CellChat, and make sure the input data are non-negative.

Thank you very much for your reply. You mean, if the gene activate matrix is ​​non-neg, there is no problem using it to run cellchat, right?