GeneNet is a package for analyzing gene expression (time series) data with focus on the inference of gene networks. In particular, GeneNet implements the methods of Sch\"afer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007) for learning large-scale gene association networks (including assignment of putative directions).
ggm.estimate.pcor, network.test.edges, extract.network, network.make.dot.