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saeyslab / nichenetr

NicheNet: predict active ligand-target links between interacting cells
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NicheNet on CIBERSORT sorted cell-populations #62

Closed cantaloupe5 closed 3 years ago

cantaloupe5 commented 3 years ago

Hello,

Thank you for creating such an amazing tool. CIBERSORTx can produce cell-type specific gene expression profiles from bulk RNA-Seq. The authors have demonstrated that their algorithm's results correlate well with FACS-sorted cell-type transcriptomes. As you have used NicheNet on FACS-sorted bulk-RNA Seq data in this paper, I was wondering what your thoughts are on using NicheNet on these "in silico" sorted cell transcriptomes. Of course, I imagine NicheNet's results will not be as reliable (as you previously said: garbage in, garbage out) but are there any reasons to avoid this technique altogether?

Thank you.

browaeysrobin commented 3 years ago

Hi @cantaloupe5 If that would be the only type of data you have to address your biological question, I think you could apply NicheNet to generate some hypotheses, but I would indeed be cautious in interpreting the results.