Gene Regulatory Networks on Single Cell RNAseq Datasets

Question

[fouerghi20]

Can I create gene regulatory network analyses on single-cell RNA-seq datasets that we haven't done any ChIP-seq or knockout of transcription factors? That is to say, are we able to overcome the sparsity of the count matrix resulting from single-cell RNA-seq and can it be done without the explicit knockout/knockdown of transcription factors?

Answer 1

[jared.andrews07]

Sure, though you should try to experimentally validate anything you find from such an analysis. You might be interested in something like NETBID2 if you have a grouping variable between samples to identify transcriptional drivers or SCENIC if not.

[fouerghi20]

Thanks for the references!