Hierarchical Network Analysis


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



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]



Chao Cheng