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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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incorporating ATAC-seq data? #60

Closed wanghlv closed 4 months ago

wanghlv commented 5 months ago

Hi I'm wondering if it's possible to incorporate the single cell ATAC-seq data? to further model on the "target" side in multi-condition/multi-sample dataset? Thanks a lot!

browaeysrobin commented 4 months ago

Hi @wanghlv

Currently there is no support for this specifically for multi-sample datasets in MultiNicheNet. In the base NicheNet package (https://github.com/saeyslab/nichenetr/blob/master/vignettes/model_construction.md) we provided a vignette where it is demonstrated how to generate your own ligand-target model. In theory, it is possible to use your scATAC-seq data to define a context-specific GRN, and thus context-specific ligand-target matrices in the end. Such a context-specific ligand-target matrix could then be used in MultiNicheNet.

However, at this stage we do not have very specific guidelines about the best way to construct context-specific GRNs based on scATAC-seq data.

wanghlv commented 4 months ago

Thank you for your suggestion, I will give a try!!