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graphite (version 1.14.1)
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
1.14.1
License
AGPL-3
Maintainer
Gabriele Sales
Last Published
June 17th, 2015
Functions in graphite (1.14.1)
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convertIdentifiers
Convert the node identifiers of a pathway.
pathways
Retrieve a list of pathways.
biocarta
BioCarta pathways
Pathways-class
Class
"Pathways"
as.list.DeprecatedPathwayList
Convertion of DeprecatedPathwayLists into lists.
as.list.PathwayList
Convertion of PathwayLists into lists.
runSPIA
Run SPIA analysis
runTopologyGSA
Run a topological analysis on an expression dataset using topologyGSA.
humancyc
Humancyc pathways
kegg
KEGG pathways
pathwayGraph
Graph representing the topology of a pathway
PathwayList-class
Class
"PathwayList"
runDEGraph
Run a topological analysis on an expression dataset using DEGraph package.
runDEGraphMulti
Run a topological analysis on an expression dataset using DEGraph package.
panther
Panther pathways
nci
NCI pathways
Pathway-class
Class
"Pathway"
pathwayDatabases
List the available pathway databases.
runTopologyGSAMulti
Run a topological analysis on an expression dataset using topologyGSA.
prepareSPIA
Prepare pathway dataset needed by runSPIA.
reactome
Reactome pathways
cytoscapePlot
Plot a pathway graph in Cytoscape
DeprecatedPathwayList-class
Class
"DeprecatedPathwayList"
runClipper
Run a topological analysis on an expression dataset using clipper.
runClipperMulti
Run a topological analysis on an expression dataset using clipper.