CoGA (Co-expression Graph Analyzer) is an R package to identify differentially co-expressed gene sets between two phenotypes. The software infers gene regulatory networks from gene expression data, and compares topological properties of the inferred networks. Those properties include centrality, clustering coefficient, degree and spectrum distributions, and spectral entropy. In addition to the differential co-expression analyses, the tool provides graphical interfaces for network visualization, ranking of genes according to their "importance" in the network, and the standard single gene differential expression analysis.
CoGA is free to use, and open source. Enjoy it!
Santos, S.S., Galatro, T.F.A., Watanabe, R.A., Oba-Shinjo, S.M., Nagahashi Marie, S.K., and Fujita, A. (2015). CoGA: An R Package to Identify Differentially Co-Expressed Gene Sets by Analyzing the Graph Spectra. PLoS ONE 10, e0135831.