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| $-method | Class '"DeprecatedPathwayList"' |
| $-method | Class '"PathwayList"' |
| as.list.DeprecatedPathwayList | Convertion of DeprecatedPathwayLists into lists. |
| as.list.PathwayList | Convertion of PathwayLists into lists. |
| biocarta | BioCarta pathways |
| convertIdentifiers | Convert the node identifiers of a pathway. |
| convertIdentifiers-method | Class '"DeprecatedPathwayList"' |
| convertIdentifiers-method | Class '"Pathway"' |
| convertIdentifiers-method | Class '"PathwayList"' |
| cytoscapePlot | Plot a pathway graph in Cytoscape |
| DeprecatedPathwayList-class | Class '"DeprecatedPathwayList"' |
| edges-method | Class '"Pathway"' |
| humancyc | Humancyc pathways |
| kegg | KEGG pathways |
| length-method | Class '"DeprecatedPathwayList"' |
| length-method | Class '"PathwayList"' |
| names-method | Class '"DeprecatedPathwayList"' |
| names-method | Class '"PathwayList"' |
| nci | NCI pathways |
| nodes-method | Class '"Pathway"' |
| panther | Panther pathways |
| Pathway-class | Class '"Pathway"' |
| pathwayDatabases | List the available pathway databases. |
| pathwayGraph | Graph representing the topology of a pathway |
| PathwayList-class | Class '"PathwayList"' |
| pathways | Retrieve a list of pathways. |
| Pathways-class | Class '"Pathways"' |
| plot-method | Class '"Pathway"' |
| prepareSPIA | Prepare pathway dataset needed by runSPIA. |
| prepareSPIA-method | Class '"DeprecatedPathwayList"' |
| prepareSPIA-method | Class '"PathwayList"' |
| prepareSPIA-method | Prepare pathway dataset needed by runSPIA. |
| reactome | Reactome pathways |
| runClipper | Run a topological analysis on an expression dataset using clipper. |
| runClipper-method | Class '"DeprecatedPathwayList"' |
| runClipper-method | Class '"Pathway"' |
| runClipper-method | Class '"PathwayList"' |
| runClipper-method | Run a topological analysis on an expression dataset using clipper. |
| runClipperMulti | Run a topological analysis on an expression dataset using clipper. |
| runDEGraph | Run a topological analysis on an expression dataset using DEGraph package. |
| runDEGraph-method | Class '"DeprecatedPathwayList"' |
| runDEGraph-method | Class '"Pathway"' |
| runDEGraph-method | Class '"PathwayList"' |
| runDEGraph-method | Run a topological analysis on an expression dataset using DEGraph package. |
| runDEGraphMulti | Run a topological analysis on an expression dataset using DEGraph package. |
| runSPIA | Run SPIA analysis |
| runTopologyGSA | Run a topological analysis on an expression dataset using topologyGSA. |
| runTopologyGSA-method | Class '"DeprecatedPathwayList"' |
| runTopologyGSA-method | Class '"Pathway"' |
| runTopologyGSA-method | Class '"PathwayList"' |
| runTopologyGSA-method | Run a topological analysis on an expression dataset using topologyGSA. |
| runTopologyGSAMulti | Run a topological analysis on an expression dataset using topologyGSA. |
| [-method | Class '"DeprecatedPathwayList"' |
| [-method | Class '"PathwayList"' |
| [[-method | Class '"DeprecatedPathwayList"' |
| [[-method | Class '"PathwayList"' |