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Inferring cell-cell interactions between cells from a scRNAseq dataset and cells from a bulk RNA seq dataset

Open livyring opened this issue 1 year ago • 0 comments

I would like to evaluate how cells within a scRNA seq dataset (tumor associated and normal adjacent fibroblast populations) may interact with cells that were isolated and ran on a bulk RNA sequencing platform (Tumor derived T cells, normal adjacent derived T cells). Is there a way to do this by inputting the DEG information of each processed dataset (ie DEGs of each cluster (fibs) and DEGs of T each cell group), or count matrices etc? is there some way to integrate both datasets such that I can do this analysis? It would be beneficial to have the expression/count data in this analysis too to infer likelihood/robustness of this predicted interaction.

If cellchat is not the tool to use for this, is there another tool that I can use wherein I input lists of DEGs based on LFC/pval cutoffs and receptor/ligand/ecm interactions are put forth?

livyring avatar Oct 25 '23 03:10 livyring