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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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Q: Is it possible to coerce bulk rna-seq data to work in CellChat? #91

Open RPSeaman opened 6 months ago

RPSeaman commented 6 months ago

Hi CellChat Team,

Thanks for making this package. My team has found it very useful as we implement it for various datasets. I am wondering if it is possible to coerce bulk RNAseq data into CellChat.

For example: Dataset 1: Bulk -- Cell Type 1 Dataset 2: Bulk -- Cell Type 2

In this case, I would ideally like to treat each bulk sample as an distinct cell types to group by in a singular CellChat object.

Is this possible?

Thanks in advance!

ManarRashad commented 5 months ago

I have the same question, Do you find any answer to that?

RPSeaman commented 5 months ago

Hi @ManarRashad No, I have yet to hear back. I did find this closed thread from their sunsetted GitHub repository. If you look at the thread starting on March 22, 2021 by "geosen," they walk through how they did it and then how they resolved the issue that they had. I have not tried this yet, but it may give you some leads. Let me know if you get it to work! Good luck