1. ROntoTools
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Browse code

added novel method and increase version to 1.99

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ROntoTools@116328 bc3139a8-67e5-0310-9ffc-ced21a209358

Calin Voichita authored on 15/04/2016 05:40:35
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NEWS
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+VERSION 2.0.0
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+--------
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+* added a novel pathway analysis method based on the primary dis-regulation of the genes in each pathway
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 VERSION 1.2.0
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Browse code

bug fixes and new feature to consider pathways with no interactions (i.e., gene sets)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ROntoTools@80800 bc3139a8-67e5-0310-9ffc-ced21a209358

Calin Voichita authored on 26/09/2013 16:41:14
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NEWS
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+VERSION 1.2.0
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+--------
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+* add the ability to analyze gene sets (pathways with no interaction) using only over-representation
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+* bug fixes: plot boundaries, etc.
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 VERSION 1.0.0
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Browse code

Add BaseSpaceR CNORfeeder eiR and ROntoTools to the repos.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ROntoTools@74711 bc3139a8-67e5-0310-9ffc-ced21a209358

Marc Carlson authored on 22/03/2013 22:40:44
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+VERSION 1.0.0
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+--------
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+Initial release of package ROntoTools includes:
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+* pe: Pathway analysis tool Pathway-Express with the following features:
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+    - perform pathway analysis on pathways defined in the standard graph format
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+provided by the package graph
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+    - perform the analysis using either differentially expressed (DE) genes or
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+using a cut-of-free analysis
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+    - when available, use both information related to the strangth of the inter-
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+action between the genes (as edgeWeights) and the relevance of each gene (as
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+nodeWeights)
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+    - the results are summerized using the generic function Summary
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+* keggPathwayGraphs/keggPathwayNames: Utility to download and parse the KEGG
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+pathways data in graph objects:
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+    - based on the work in the packages KEGGREST and KEGGgraph
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+* nodeWeigths: the missing generic convenience function from package graph to
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+get the node weights of a graph
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+* alpha1MR/alphaMLG: two utilites to transform the a vector of p-values into
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+weights to be used as nodeWeights
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