clipper

Package: clipper
Version: 1.12.0
Date: 2015-08-31
Title: Gene Set Analysis Exploiting Pathway Topology
Author: Paolo Martini <paolo.cavei@gmail.com>, Gabriele Sales <gabriele.sales@unipd.it>, Chiara Romualdi <chiara.romualdi@unipd.it>
Maintainer: Paolo Martini <paolo.cavei@gmail.com>
Description: Implements topological gene set analysis using a two-step empirical approach. It exploits graph decomposition theory to create a junction tree and reconstruct the most relevant signal path. In the first step clipper selects significant pathways according to statistical tests on the means and the concentration matrices of the graphs derived from pathway topologies. Then, it "clips" the whole pathway identifying the signal paths having the greatest association with a specific phenotype.
Depends: R (>= 2.15.0), Matrix, graph
Imports: methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph,
KEGGgraph, corpcor, RBGL
Suggests: RUnit, BiocGenerics, RCytoscape (>= 1.6.3), graphite, ALL,
hgu95av2.db, MASS, BiocStyle
License: AGPL-3
NeedsCompilation: no
Packaged: 2016-05-04 04:50:32 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'clipper' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'clipper'
    finding HTML links ... done
    clipper                                 html  
    clipperAllRoots                         html  
    cliqueMeanTest                          html  
    cliqueMixedTest                         html  
    cliquePairedTest                        html  
    cliqueVarianceTest                      html  
    deleteEdge                              html  
    easyClip                                html  
    easyLook                                html  
    getGraphEntryGenes                      html  
    getJunctionTreePaths                    html  
    nameCliques                             html  
    pathwayTest                             html  
    plotInCytoscape                         html  
    prunePaths                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (clipper)
Making 'packages.html' ... done