VERSION 2.0.0 -------- * added a novel pathway analysis method based on the primary dis-regulation of the genes in each pathway VERSION 1.2.0 -------- * add the ability to analyze gene sets (pathways with no interaction) using only over-representation * bug fixes: plot boundaries, etc. VERSION 1.0.0 -------- Initial release of package ROntoTools includes: * pe: Pathway analysis tool Pathway-Express with the following features: - perform pathway analysis on pathways defined in the standard graph format provided by the package graph - perform the analysis using either differentially expressed (DE) genes or using a cut-of-free analysis - when available, use both information related to the strangth of the inter- action between the genes (as edgeWeights) and the relevance of each gene (as nodeWeights) - the results are summerized using the generic function Summary * keggPathwayGraphs/keggPathwayNames: Utility to download and parse the KEGG pathways data in graph objects: - based on the work in the packages KEGGREST and KEGGgraph * nodeWeigths: the missing generic convenience function from package graph to get the node weights of a graph * alpha1MR/alphaMLG: two utilites to transform the a vector of p-values into weights to be used as nodeWeights