graphite: GRAPH Interaction from pathway Topological Environment

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

AuthorGabriele Sales <gabriele.sales@unipd.it>, Enrica Calura <enrica.calura@gmail.com>, Chiara Romualdi <chiara.romualdi@unipd.it>
Date of publicationNone
MaintainerGabriele Sales <gabriele.sales@unipd.it>
LicenseAGPL-3
Version1.20.1

View on Bioconductor

Functions

as.list.DeprecatedPathwayList Man page
as.list.PathwayList Man page
biocarta Man page
buildPathway Man page
convertIdentifiers Man page
convertIdentifiers,DeprecatedPathwayList-method Man page
convertIdentifiers,PathwayList-method Man page
convertIdentifiers,Pathway-method Man page
cytoscapePlot Man page
DeprecatedPathwayList-class Man page
[,DeprecatedPathwayList-method Man page
[[,DeprecatedPathwayList-method Man page
$,DeprecatedPathwayList-method Man page
edges,Pathway,ANY-method Man page
humancyc Man page
kegg Man page
length,DeprecatedPathwayList-method Man page
length,PathwayList-method Man page
names,DeprecatedPathwayList-method Man page
names,PathwayList-method Man page
nci Man page
nodes,Pathway-method Man page
panther Man page
Pathway-class Man page
pathwayDatabases Man page
pathwayGraph Man page
PathwayList-class Man page
[,PathwayList-method Man page
[[,PathwayList-method Man page
$,PathwayList-method Man page
pathways Man page
Pathways-class Man page
plot,Pathway,ANY-method Man page
prepareSPIA Man page
prepareSPIA,DeprecatedPathwayList-method Man page
prepareSPIA,list-method Man page
prepareSPIA,PathwayList-method Man page
reactome Man page
runClipper Man page
runClipper,DeprecatedPathwayList-method Man page
runClipper,list-method Man page
runClipperMulti Man page
runClipper,PathwayList-method Man page
runClipper,Pathway-method Man page
runDEGraph Man page
runDEGraph,DeprecatedPathwayList-method Man page
runDEGraph,list-method Man page
runDEGraphMulti Man page
runDEGraph,PathwayList-method Man page
runDEGraph,Pathway-method Man page
runSPIA Man page
runTopologyGSA Man page
runTopologyGSA,DeprecatedPathwayList-method Man page
runTopologyGSA,list-method Man page
runTopologyGSAMulti Man page
runTopologyGSA,PathwayList-method Man page
runTopologyGSA,Pathway-method Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.