biocarta | BioCarta pathways |
convertIdentifiers | Convert the node identifiers of a pathway. |
cytoscapePlot | Plot a pathway graph in Cytoscape |
edges-method | Class '"pathway"' |
kegg | KEGG pathways |
nci | NCI pathways |
nodes-method | Class '"pathway"' |
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 |