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graphite (version 1.16.0)
GRAPH Interaction from pathway Topological Environment
Description
Graph objects from pathway topology derived from Biocarta, HumanCyc, KEGG, NCI, Panther, Reactome and SPIKE databases.
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1.18.0
1.16.0
1.14.1
1.12.0
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Monthly Downloads
22
Version
1.16.0
License
AGPL-3
Maintainer
Gabriele Sales
Last Published
October 7th, 2015
Functions in graphite (1.16.0)
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nci
NCI pathways
panther
Panther pathways
Pathways-class
Class
"Pathways"
pathways
Retrieve a list of pathways.
kegg
KEGG pathways
humancyc
Humancyc pathways
runClipper
Run a topological analysis on an expression dataset using clipper.
runClipperMulti
Run a topological analysis on an expression dataset using clipper.
runDEGraph
Run a topological analysis on an expression dataset using DEGraph package.
runDEGraphMulti
Run a topological analysis on an expression dataset using DEGraph package.
as.list.DeprecatedPathwayList
Convertion of DeprecatedPathwayLists into lists.
as.list.PathwayList
Convertion of PathwayLists into lists.
reactome
Reactome pathways
prepareSPIA
Prepare pathway dataset needed by runSPIA.
biocarta
BioCarta pathways
convertIdentifiers
Convert the node identifiers of a pathway.
PathwayList-class
Class
"PathwayList"
runSPIA
Run SPIA analysis
runTopologyGSA
Run a topological analysis on an expression dataset using topologyGSA.
pathwayGraph
Graph representing the topology of a pathway
cytoscapePlot
Plot a pathway graph in Cytoscape
Pathway-class
Class
"Pathway"
DeprecatedPathwayList-class
Class
"DeprecatedPathwayList"
pathwayDatabases
List the available pathway databases.
runTopologyGSAMulti
Run a topological analysis on an expression dataset using topologyGSA.