related scripts or equations for implementing analyses in paper “Genomic analysis of the hierarchical structure of regulatory networks”

Q:
I recently have been working on constructing human regulatory networks. After reading your paper <Genomic analysis of the hierarchical structure of regulatory networks> published on PNAS, I found it very amazing and useful, which may be applied for my study. I want to construct hierarchical structure of transcription factors (TFs) in humans, and my data is the expression level of these TFs and their targets obtained by RNA sequencing. Can we use your BFS method to construct the network? As we know little about the computational algorithm of BFS, would you please provide related scripts or equations for implementing it easily?

Thank you very much for occupying your precious time reading my letter and I’m looking forward to your guidance.

A:
Hi, see http://info.gersteinlab.org/Hierarchy

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