Hi everyone!

I am doing RNA-sequencing with the DESeq2 package and wanted to look at some transcription factor activity. For that I am using the run_viper() function from the decoupleR package, with the collectri network as a reference for TF-targets.

But I am not quite sure, in which format I should provide my expression data to the function. A lot of values might make sense/are possible according to the documentation:

decoupleR needs a matrix (mat) of any molecular readouts (gene expression, logFC, p-values, etc.) and a network that relates target features

So far I've provided either:

1. normalized counts from DESeq
2. z-scores of transformed counts (using vst)

The second option intuitively makes more sense to me, but I would love other opinions.

Thanks! Julian