graphite: GRAPH Interaction from pathway Topological Environment
Version 1.22.0

Graph objects from pathway topology derived from Biocarta, HumanCyc, KEGG, NCI, Panther, Reactome and SPIKE databases.

Browse man pages Browse package API and functions Browse package files

AuthorGabriele Sales <gabriele.sales@unipd.it>, Enrica Calura <enrica.calura@gmail.com>, Chiara Romualdi <chiara.romualdi@unipd.it>
Bioconductor views BioCarta GraphAndNetwork KEGG Network Pathways Reactome ThirdPartyClient
Date of publicationNone
MaintainerGabriele Sales <gabriele.sales@unipd.it>
LicenseAGPL-3
Version1.22.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("graphite")

Man pages

as.list.DeprecatedPathwayList: Convertion of DeprecatedPathwayLists into lists.
as.list.PathwayList: Convertion of PathwayLists into lists.
biocarta: BioCarta pathways
buildPathway: Build a Pathway object.
convertIdentifiers: Convert the node identifiers of a pathway.
cytoscapePlot: Plot a pathway graph in Cytoscape
DeprecatedPathwayList-class: Class '"DeprecatedPathwayList"'
humancyc: Humancyc pathways
kegg: KEGG pathways
nci: NCI pathways
panther: Panther pathways
Pathway-class: Class '"Pathway"'
pathwayDatabases: List the available pathway databases.
pathwayGraph: Graph representing the topology of a pathway
PathwayList-class: Class '"PathwayList"'
pathways: Retrieve a list of pathways.
Pathways-class: Class '"Pathways"'
prepareSPIA: Prepare pathway dataset needed by runSPIA.
reactome: Reactome pathways
runClipper: Run a topological analysis on an expression dataset using...
runClipperMulti: Run a topological analysis on an expression dataset using...
runDEGraph: Run a topological analysis on an expression dataset using...
runDEGraphMulti: Run a topological analysis on an expression dataset using...
runSPIA: Run SPIA analysis
runTopologyGSA: Run a topological analysis on an expression dataset using...
runTopologyGSAMulti: Run a topological analysis on an expression dataset using...

Functions

$,DeprecatedPathwayList-method Man page
$,PathwayList-method Man page
DeprecatedPathwayList-class Man page
Pathway-class Man page
PathwayList-class Man page
Pathways-class Man page
[,DeprecatedPathwayList-method Man page
[,PathwayList-method Man page
[[,DeprecatedPathwayList-method Man page
[[,PathwayList-method Man page
archiveDir Source code
as.list.DeprecatedPathwayList Man page Source code
as.list.PathwayList Man page Source code
biocarta Man page
buildGraphNEL Source code
buildPathway Man page Source code
canonicalEdgeNames Source code
checkEdgeTypes Source code
checkIdentifier Source code
checkPathwayList Source code
checkPkgVersion Source code
checkTitle Source code
clipper Source code
clipperList Source code
convert Source code
convertIdentifiers Man page
convertIdentifiers,DeprecatedPathwayList-method Man page
convertIdentifiers,Pathway-method Man page
convertIdentifiers,PathwayList-method Man page
cytoscapePlot Man page Source code
cytoscapePlot2 Source code
cytoscapePlot3 Source code
datasetName Source code
degraph Source code
degraphList Source code
deprecatedFn Source code
deprecatedObj Source code
destIdentifier Source code
edgeList Source code
edges,Pathway,ANY-method Man page
filterByTag Source code
filterPathwaysByNodeNum Source code
fixEdges Source code
humancyc Man page
initClipper Source code
initDEGraph Source code
initTopologyGSA Source code
insufficientCommonGenes Source code
kegg Man page
lapplyCapturingErrors Source code
length,DeprecatedPathwayList-method Man page
length,PathwayList-method Man page
loadDb Source code
loadLocal Source code
loadRemote Source code
localArchive Source code
lookupKeys Source code
markMultiple Source code
mergeEdges Source code
names,DeprecatedPathwayList-method Man page
names,PathwayList-method Man page
nci Man page
nodes,Pathway-method Man page
panther Man page
pathwayDatabases Man page Source code
pathwayGraph Man page Source code
pathways Man page Source code
plot,Pathway,ANY-method Man page
prepareEdges Source code
prepareSPIA Man page Source code
prepareSPIA,DeprecatedPathwayList-method Man page
prepareSPIA,PathwayList-method Man page
prepareSPIA,list-method Man page
prettyDate Source code
reactome Man page
requirePkg Source code
runClipper Man page
runClipper,DeprecatedPathwayList-method Man page
runClipper,Pathway-method Man page
runClipper,PathwayList-method Man page
runClipper,list-method Man page
runClipperMulti Man page Source code
runDEGraph Man page
runDEGraph,DeprecatedPathwayList-method Man page
runDEGraph,Pathway-method Man page
runDEGraph,PathwayList-method Man page
runDEGraph,list-method Man page
runDEGraphMulti Man page Source code
runSPIA Man page Source code
runTopologyGSA Man page
runTopologyGSA,DeprecatedPathwayList-method Man page
runTopologyGSA,Pathway-method Man page
runTopologyGSA,PathwayList-method Man page
runTopologyGSA,list-method Man page
runTopologyGSAMulti Man page Source code
selectDb Source code
selectEdges Source code
switchTest Source code
symmetricEdges Source code
topologyGSA Source code
topologyGSAList Source code
translateEdges Source code

Files

DESCRIPTION
NAMESPACE
R
R/build.R
R/clipper.R
R/conversion.R
R/degraph.R
R/fetch.R
R/graph.R
R/pathway.R
R/plot.R
R/spia.R
R/tables.R
R/topologygsa.R
R/utils.R
build
build/vignette.rds
data
data/datalist
data/pathways.RData
inst
inst/NEWS
inst/doc
inst/doc/graphite.R
inst/doc/graphite.Rnw
inst/doc/graphite.pdf
man
man/DeprecatedPathwayList-class.Rd
man/Pathway-class.Rd
man/PathwayList-class.Rd
man/Pathways-class.Rd
man/as.list.DeprecatedPathwayList.Rd
man/as.list.PathwayList.Rd
man/biocarta.Rd
man/buildPathway.Rd
man/convertIdentifiers.Rd
man/cytoscapePlot.Rd
man/humancyc.Rd
man/kegg.Rd
man/nci.Rd
man/panther.Rd
man/pathwayDatabases.Rd
man/pathwayGraph.Rd
man/pathways.Rd
man/prepareSPIA.Rd
man/reactome.Rd
man/runClipper.Rd
man/runClipperMulti.Rd
man/runDEGraph.Rd
man/runDEGraphMulti.Rd
man/runSPIA.Rd
man/runTopologyGSA.Rd
man/runTopologyGSAMulti.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_build.R
tests/testthat/test_conversion.R
vignettes
vignettes/Cytoscape.png
vignettes/graphite.Rnw
graphite documentation built on May 20, 2017, 10:47 p.m.