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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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How to use bulk RNASeq data? #37

Closed akiss-me closed 10 months ago

akiss-me commented 10 months ago

Hi, thank you for the brilliant tool! I have 8 bulk RNASeq samples (4 control, 4 treated). Can I use multinichenet to analyze it?

browaeysrobin commented 10 months ago

Hi @akiss-me

In case you have bulk RNA-seq of sorted cell populations, yes. You can use the same pipeline and ideas, but instead of the pseudobulk DE and expression, you can use your bulk expression. You will have to change the corresponding functions yourself, though, since we are not going to support/maintain this.