How to run Aracne cytoscape plugin ?
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3.6 years ago

I'm intended to infer Gene Regulatory Network (GRN) using ARACNE algorithm and using gene expression matrix. I already have a gene expression matrix file and a list of TFs. But I'm not able to understand how to import in Cytoscape and draw network using ARACNE. Do I have to draw the GRN using any other software and then use ARACNE or does ARACNE does everything from the scratch?

I'm completely new in this field. Any help would be really appreciated.

R rna-seq cytoscape • 1.4k views
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@prithvi.mastermind have you been able to find a solution to this? if so, could you share how you did it?

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5 months ago
Scooter ▴ 280

From a very brief glance at the code, it looks like all you need to do is to load a network (not necessarily a GRN) with your genes, add your expression data to it, then use ARACNe to calculate the GRN. As near as I can tell it will provide results in a table, which you can then use to style the network.

-- scooter

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