graphite: GRAPH Interaction from pathway Topological Environment

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

Author
Gabriele Sales <gabriele.sales@unipd.it>, Enrica Calura <enrica.calura@gmail.com>, Chiara Romualdi <chiara.romualdi@unipd.it>
Date of publication
None
Maintainer
Gabriele Sales <gabriele.sales@unipd.it>
License
AGPL-3
Version
1.20.1

View on Bioconductor

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...

Files in this package

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