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PySCENIC - Running on a single TF?

Hello,

I am studying a particular transcription factor of interest and am new to gene regulatory network analysis methods. I would like to use SCENIC to infer regulon activity from my scRNA data. I know that each SCENIC run takes a long time (especially the GRN step), so if one would like to have many replicates it can be quite time-consuming.

I also know that one can limit the number of TFs in the input TF list to speed things up. Therefore I was wondering if it would make sense to input solely the one TF I am interested in, so that I can hopefully run say >1000 times to get very robust statistics? Would such an approach make sense, or would it violate any model assumptions? Would the GRN construction in this case indeed be super fast? Has this approach been done before?

Thanks in advance, Joshua

grn transcription_factor scenic transcriptomics
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updated by Arup Ghosh Arup Ghosh • written by joshua.rubin • joshua.rubin

1 answer

It will defeat the purpose of the SCENIC analysis. The sole TF will be assigned as the only contributor for all the gene expression profiles.

If you have access to an HPC cluster, try: https://github.com/vib-singlecell-nf/vsn-pipelines

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written by Arup Ghosh Arup Ghosh

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