**Hierarchical Network Analysis**

**About**

**HierNet is a simulated annealing algorithm to determine the hierarchical structure and calculate the hierarchy score of a directed network. **

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R functions R functions for determining hieararchical structure, calculating hierarchy scores, optimizing parameters of a given directed network.

Sample R code An example to show how to run the R functions.

Sample network data An example network containing yeast transcription factor interactions identified based on ChIP-chip experiments.

Sample output file An example output file.

An Approach for Determining and Measuring Network Hierarchy: Application to Comparing the Phosphorylome and the Regulome. Cheng C

^{$}, Andrews E, Yan K, Ung M, Wang D, Gerstein M^{$}.Genome Biol.2015. [Pubmed]

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