Package: keggorthology
Title: graph support for KO, KEGG Orthology
Version: 2.24.0
Author: VJ Carey <stvjc@channing.harvard.edu>
Description: graphical representation of the Feb 2010 KEGG Orthology.
The KEGG orthology is a set of pathway IDs that are not to be
confused with the KEGG ortholog IDs.
Depends: R (>= 2.5.0), stats, graph, hgu95av2.db
Imports: AnnotationDbi, graph, DBI, graph, grDevices, methods, stats, tools, utils
Suggests: RBGL, ALL
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
License: Artistic-2.0
biocViews: Pathways, GraphAndNetwork, Visualization, KEGG
NeedsCompilation: no
Packaged: 2016-05-04 03:01:05 UTC; biocbuild
Package: ddgraph
Imports: bnlearn (>= 2.8), gtools, pcalg, RColorBrewer, plotrix, MASS
Maintainer: Robert Stojnic <robert.stojnic@gmail.com>
License: GPL-3
Title: Distinguish direct and indirect interactions with Graphical
Modelling
LinkingTo: Rcpp
Type: Package
LazyLoad: yes
Author: Robert Stojnic
Description: Distinguish direct from indirect interactions in gene
regulation and infer combinatorial code from highly correlated
variables such as transcription factor binding profiles. The
package implements the Neighbourhood Consistent PC algorithm
(NCPC) and draws Direct Dependence Graphs to represent
dependence structure around a target variable. The package also
provides a unified interface to other Graphical Modelling
(Bayesian Network) packages for distinguishing direct and
indirect interactions.
Version: 1.16.0
Date: 2015-01-27
Depends: graph, methods, Rcpp
Suggests: Rgraphviz, e1071, ROCR, testthat
Collate: 'AllClassses.R' 'AllGenerics.R' 'calcDependence.R' 'citest.R'
'combinations.R' 'dsep.R' 'furlong.R' 'methods-CITestResult.R'
'methods-DDDataSet.R' 'methods-DDGraphEdge.R'
'methods-DDGraph.R' 'misc.R' 'ncpc.R' 'other-algorithms.R'
'plot-colour.R' 'plot.R' 'randomnet.R' 'resampling.R' 'svm.R'
biocViews: GraphAndNetwork
NeedsCompilation: yes
Packaged: 2016-05-04 04:31:38 UTC; biocbuild
Package: topGO
Type: Package
Title: Enrichment Analysis for Gene Ontology
Version: 2.24.0
Date: 2016-02-03
Author: Adrian Alexa, Jorg Rahnenfuhrer
Maintainer: Adrian Alexa <adrian.alexa@gmail.com>
Description: topGO package provides tools for testing GO terms while
accounting for the topology of the GO graph. Different test
statistics and different methods for eliminating local
similarities and dependencies between GO terms can be
implemented and applied.
License: LGPL
Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.6), graph (>=
1.14.0), Biobase (>= 2.0.0), GO.db (>= 2.3.0), AnnotationDbi
(>= 1.7.19), SparseM (>= 0.73)
Imports: lattice, matrixStats, DBI
Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest
Collate: AllClasses.R topGOmethods.R topGOgraph.R topGOalgo.R
topGOfunctions.R topGOannotations.R topGOtests.R topGOviz.R
zzz.R
biocViews: Microarray, Visualization
NeedsCompilation: no
Packaged: 2016-05-04 03:00:37 UTC; biocbuild
Package: pkgDepTools
Type: Package
Title: Package Dependency Tools
Version: 1.38.0
Author: Seth Falcon
Maintainer: Seth Falcon <seth@userprimary.net>
Description: This package provides tools for computing and analyzing
dependency relationships among R packages. It provides tools
for building a graph-based representation of the dependencies
among all packages in a list of CRAN-style package
repositories. There are also utilities for computing
installation order of a given package. If the RCurl package is
available, an estimate of the download size required to install
a given package and its dependencies can be obtained.
License: GPL-2
Depends: methods, graph, RBGL
Imports: graph, RBGL
Suggests: Biobase, Rgraphviz, RCurl, BiocInstaller
LazyLoad: Yes
biocViews: Infrastructure, GraphAndNetwork
NeedsCompilation: no
Packaged: 2016-05-04 02:58:19 UTC; biocbuild
Package: ppiData
Title: A package that contains the bait to prey directed graphs for
protein-protein interactions.
Version: 0.10.0
Author: Tony Chiang
LazyLoad: TRUE
LazyData: TRUE
Depends: graph
Imports: AnnotationDbi
Suggests: org.Sc.sgd.db, ppiStats
Description: This package contains the directed graphs for protein interaction data as derived from Y2H and APMS as well as the code used to obtain the y2h data from IntAct Repository.
biocViews: ExperimentData
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
License: Artistic-2.0
NeedsCompilation: no
Packaged: 2016-05-07 20:12:14 UTC; biocbuild
Package: yeastExpData
Title: Yeast Experimental Data
Version: 0.18.0
Author: R. Gentleman
Description: A collection of different sets of experimental data from yeast.
biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data
Maintainer: R. Gentleman <rgentlem@fhcrc.org>
License: GPL
Depends: R (>= 2.4), graph (>= 1.9.26)
Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db
NeedsCompilation: no
Packaged: 2016-05-07 20:12:25 UTC; biocbuild
Package: GraphAT
Title: Graph Theoretic Association Tests
Version: 1.44.0
Date: 2012-04-27
Author: R. Balasubramanian, T. LaFramboise, D. Scholtens
Description: Functions and data used in Balasubramanian, et al. (2004)
Maintainer: Thomas LaFramboise <tlaframb@hsph.harvard.edu>
Depends: R (>= 2.10), graph, methods
Imports: graph, MCMCpack, methods, stats
License: LGPL
biocViews: Network, GraphAndNetwork
NeedsCompilation: no
Packaged: 2016-05-04 02:41:45 UTC; biocbuild
providing 
.