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saeyslab / multinichenetr

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
GNU General Public License v3.0
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Question #62

Closed nicolebussola closed 4 months ago

nicolebussola commented 4 months ago

Hi!

Thank you for this great tool, looking forward to the next release for condition-specific cell types! I am currently analyzing two datasets with the same condition and I am interested in finding reproducible signals. Thus, I am setting the weight for DE to 0 as I am looking for similarities and not differences; I am not sure on how to deal with ligand activity as it considers genesets output by the DE analysis. Can I weight the L-R pairs to have a high activity based on target genes that are not DE? Do you have any other suggestions I should keep in mind?

Thanks Nicole

browaeysrobin commented 4 months ago

Hi @nicolebussola

MultiNicheNet has been designed to specifically analyze differential cell-cell communication patterns. Every part of the algorithms serves to prioritize which signals are different between your conditions. Therefore, I recommend against using MultiNicheNet for your application (and I will close this issue). I suggest you try out classic CCC tools on each of your datasets, and look at the intersection of the top results there.