KEGGgraph

Package: KEGGgraph
Type: Package
Title: KEGGgraph: A graph approach to KEGG PATHWAY in R and
Bioconductor
Version: 1.30.0
Date: 2015-05-25
Author: Jitao David Zhang, with inputs from Paul Shannon
Maintainer: Jitao David Zhang <jitao_david.zhang@roche.com>
Description: KEGGGraph is an interface between KEGG pathway and graph
object as well as a collection of tools to analyze, dissect and
visualize these graphs. It parses the regularly updated KGML
(KEGG XML) files into graph models maintaining all essential
pathway attributes. The package offers functionalities
including parsing, graph operation, visualization and etc.
License: GPL (>= 2)
LazyLoad: yes
Depedence: R (>=2.10)
Imports: methods, XML (>= 2.3-0), graph
Suggests: Rgraphviz, RBGL, RUnit, RColorBrewer, KEGG.db, org.Hs.eg.db,
hgu133plus2.db, SPIA
Collate: kegg2graph-functions.R parse.R annotation.R graph.R kgmlfile.R
misc.R vis.R
URL: http://www.nextbiomotif.com
biocViews: Pathways, GraphAndNetwork, Visualization, KEGG
NeedsCompilation: no
Packaged: 2016-05-04 03:11:17 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'KEGGgraph' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'KEGGgraph'
    finding HTML links ... done
    KEGGEdge-class                          html  
    KEGGEdgeSubType-class                   html  
    KEGGEdgeSubtype                         html  
    KEGGGraphics-class                      html  
    KEGGGroup-class                         html  
    KEGGNode-class                          html  
    KEGGPathway-class                       html  
    KEGGPathwayInfo-class                   html  
    KEGGReaction-class                      html  
    KEGGpathway2Graph                       html  
    KEGGpathway2reactionGraph               html  
    expandKEGGNode                          html  
    expandKEGGPathway                       html  
    getDisplayName-methods                  html  
    getEntryID-methods                      html  
    getKEGGID-methods                       html  
    getKEGGgeneLink-methods                 html  
    getKEGGnodeData                         html  
    getKGMLurl                              html  
    getName-methods                         html  
    getNamedElement                         html  
    getPathwayInfo-methods                  html  
    getReactions-methods                    html  
    getRgraphvizEdgeNames                   html  
    getSubtype-methods                      html  
    getTitle-methods                        html  
    getType-methods                         html  
    getValue-methods                        html  
    graphDensity                            html  
    isHomoList                              html  
    kgmlFileName2PathwayName                html  
    mergeGraphs                             html  
    mergeKEGGgraphs                         html  
    neighborhood                            html  
    parseEntry                              html  
    parseGraphics                           html  
    parseKGML                               html  
    parseKGML2DataFrame                     html  
    parseKGML2Graph                         html  
    parseKGMLexpandMaps                     html  
    parsePathwayInfo                        html  
    parseReaction                           html  
    parseRelation                           html  
    parseSubType                            html  
    plotKEGGgraph                           html  
    pvalue2asterisk                         html  
    queryKEGGsubgraph                       html  
    randomSubGraph                          html  
    splitKEGGgroup                          html  
    subGraphByNodeType                      html  
    subKEGGgraph                            html  
    subtypeDisplay-methods                  html  
    top                                     html  
    translateKEGGID2GeneID                  html  
    translateKEGGgraph                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (KEGGgraph)
Making 'packages.html' ... done