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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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no sample_id #41

Closed GGboy-Zzz closed 9 months ago

GGboy-Zzz commented 9 months ago

hi,can i define "sample_id" = NA or others, so ignore this parameter？

browaeysrobin commented 9 months ago

Hi @GGboy-Zzz

This is not possible since MultiNicheNet is a method explicitly taking into account sample-to-sample variability.

GGboy-Zzz commented 9 months ago

thanks your reply! @browaeysrobin I browsed all [vignettes] in nichenetr, and I cant find a methods to infer cell-cell interactions from multiple receiver. My data is about embryonic development, there are significant differences in cell types at different stages, can you give me some suggestions about how to perform nichenetr analysis pipeline?

browaeysrobin commented 9 months ago

Hi @GGboy-Zzz

Short answer: NicheNet is a receiver cell type - focused pipeline. You should thus run a NicheNet analysis for one receiver at the time. Once you have set up your analysis pipeline for one receiver, you can of course write a wrapper so the analysis happens for all cell types of interest in your data.

For further questions concerning nichenetr, you should open a github issue there and not here since this is here multinichenetr.

GGboy-Zzz commented 9 months ago

Okay, thank you very much