VERSION 2.0.0
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 * added a novel pathway analysis method based on the primary dis-regulation of the genes in each pathway
 

 VERSION 1.2.0
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 * add the ability to analyze gene sets (pathways with no interaction) using only over-representation
 * bug fixes: plot boundaries, etc.

 
 VERSION 1.0.0
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 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