biocarta                BioCarta pathways
convertIdentifiers      Convert the node identifiers of a pathway.
cytoscapePlot           Plot a pathway graph in Cytoscape
kegg                    KEGG pathways
nci                     NCI 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.
spike                   SPIKE pathways
