CoGA

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 structural properties of the inferred networks based on their spectrum distributions. It also compares the networks in terms of their gene centralities, clustering coefficients and shortest path lengths. 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.