Closed nicolebussola closed 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.
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