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PayamDiba / SERGIO

A simulator for single-cell expression data guided by gene regulatory networks
GNU General Public License v3.0
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PyScenic Guidance #13

Open roivant-matts opened 3 years ago

roivant-matts commented 3 years ago

Hello, Thanks for your research and tool. Do you have any guidance or work already done for formatting SERGIO build_graph input from PyScenic output? A couple of us did some preliminary review and were not able to have a quick solution. To have an idea of a pyscenic workflow, check here: https://github.com/aertslab/pySCENIC/blob/master/notebooks/pySCENIC%20-%20Full%20pipeline.ipynb

Best regards, Matt

ghost commented 3 years ago

Hello, it's where I am currently stacked. I have generated the GRN with PyScenic, but I have a hard time adapting its output to the input for SERGIO to synthesize new data. Any help with it? This is how the PyScenic GRN looks like: image

But I don't understand how to format and use the hill function. Does the importance column have to be converted with the hill function?

In the paper, SERGIO mentions they use GENIE3 and GNW to do inference to the GRN, but I don't see the script here that does such processing to make it work with SERGIO.

PayamDiba commented 2 years ago

Sorry, I just saw these posts. Could you figure out any solution?

pierrechemla commented 2 years ago

Hi,

I am also interested using GENIE3 for GRN inference and couldn't find out how to process the GRN outputs for Sergio. Did you figure out how to process GENIE3 GRN outputs for Sergio inputs ?

Thanks,

Pierre