Many topological properties of networks can be succinctly described using network concepts, also known as network statistics or indices [11,33]. Network concepts include whole network connectivity (degree), intramodular connectivity, topological overlap, the clustering coefficient, density etc. Differential analysis of network concepts such as intramodular connectivity may reveal regulatory changes in gene expressions [15,18]. The WGCNA package implements several functions, such as softConnectivity, intramodularConnectivity, TOMSimilarity, clusterCoef, networkConcepts, for computing these network concepts. Basic R functions can be used to create summary statistics of these concepts and for testing their differences across networks.
