The PathNet package and its associated experimental data package PathNetData are now available in the BioC development branch.
PathNet uses topological information present in pathways and differential expression levels of genes (obtained from microarray experiment) to identify pathways that are 1) significantly enriched and 2) associated with each other in the context of differential expression. The algorithm is described in: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J. Source Code for Biology and Medicine 2012 Sep 24;7(1):10. BioC page for PathNet: http://bioconductor.org/packages/2.12/bioc/html/PathNet.html BioC page for PathNetData: http://bioconductor.org/packages/2.12/data/experiment/html/PathNetData.html Thanks, Jason Smith Software Developer, HJF Biotechnology HPC Software Applications Institute _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
