NEWS

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ROntoTools 2.0.0

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

ROntoTools 1.2.0

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

ROntoTools 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