GRAPH Interaction from pathway Topological Environment


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Documentation for package ‘graphite’ version 1.12.0

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biocarta BioCarta pathways
convertIdentifiers Convert the node identifiers of a pathway.
cytoscapePlot Plot a pathway graph in Cytoscape
edges-method Class '"pathway"'
humancyc Humancyc pathways
kegg KEGG pathways
nci NCI pathways
nodes-method Class '"pathway"'
panther Panther pathways
pathway-class Class '"pathway"'
pathwayGraph Graph representing the topology of a pathway
prepareSPIA Prepare pathway dataset needed by runSPIA.
reactome Reactome pathways
runClipper Run a topological analysis on an expression dataset using the clipper.
runClipperMulti Run topological analyses on an expression dataset, calling clipper over all the pathways in a list.
runDEGraph Run a topological analysis on an expression dataset using DEGraph package.
runDEGraphMulti Run topological analyses on an expression dataset, calling DEGraph over all the pathways in a list.
runSPIA Run SPIA analysis
runTopologyGSA Run a topological analysis on an expression dataset using topologyGSA.
runTopologyGSAMulti Run topological analyses on an expression dataset, calling topologyGSA over all the pathways in a list.
show-method Class '"pathway"'
spike SPIKE pathways