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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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Use on multiple samples but no different conditions #38

Closed nvribeiro closed 10 months ago

nvribeiro commented 10 months ago

Hi NicheNet team!

I have more of a conceptual question and I was wondering if you could help me with that. I am working with a dataset that has 5 disease and 5 control samples. Because I have some cell types that are disease-specific, I can't use the comparison disease vs control in MultiNicheNet because I won't have the cells in control to compare to. So, I was thinking about running the pipeline on the different groups separately and see what is different. Is it possible to use MultiNicheNet in just one group with multiple samples to correct for covariates and inter-sample variation? Should I just run the standard pipeline without defining the contrasts? Or should I use the original NicheNet implementation? What would you advise in this case?

Thank you very much! Kind regards, Nathan

browaeysrobin commented 10 months ago

Hi @nvribeiro

MultiNicheNet is really specifically designed for differential CCC analysis between conditions, so you cannot run (an adaptation of) the pipeline on conditions individually. Depending on your data/research questions, starting from the original NicheNet and tweaking the pipeline there may be possible.

Related to this, you can check issue #32 and the solution I propose there; we will be releasing a work-around to handle condition-specific cell types soon (within one month).

To summarize: it's not possible to use MultiNicheNet without specifying conditions/comparisons (that's why I will be closing this issue) -- for more questions/discussion about handling condition-specific cell types, I refer you to #32