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graphite (version 1.12.0)
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
1.12.0
License
AGPL-3
Maintainer
Gabriele Sales
Last Published
October 2nd, 2014
Functions in graphite (1.12.0)
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kegg
KEGG pathways
runTopologyGSAMulti
Run topological analyses on an expression dataset, calling topologyGSA over all the pathways in a list.
nci
NCI pathways
runTopologyGSA
Run a topological analysis on an expression dataset using topologyGSA.
pathwayGraph
Graph representing the topology of a pathway
prepareSPIA
Prepare pathway dataset needed by runSPIA.
convertIdentifiers
Convert the node identifiers of a pathway.
biocarta
BioCarta pathways
reactome
Reactome pathways
runClipper
Run a topological analysis on an expression dataset using the clipper.
cytoscapePlot
Plot a pathway graph in Cytoscape
runClipperMulti
Run topological analyses on an expression dataset, calling clipper over all the pathways in a list.
humancyc
Humancyc pathways
runDEGraph
Run a topological analysis on an expression dataset using DEGraph package.
panther
Panther pathways
pathway-class
Class
"pathway"
runSPIA
Run SPIA analysis
runDEGraphMulti
Run topological analyses on an expression dataset, calling DEGraph over all the pathways in a list.
spike
SPIKE pathways