$-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 |
buildPathway | Build a Pathway object. |
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"' |
pathwayDatabase | Class '"Pathway"' |
pathwayDatabases | List the available pathway databases. |
pathwayGraph | Graph representing the topology of a pathway |
pathwayId | Class '"Pathway"' |
PathwayList-class | Class '"PathwayList"' |
pathways | Retrieve a list of pathways. |
Pathways-class | Class '"Pathways"' |
pathwaySpecies | Class '"Pathway"' |
pathwayTimestamp | Class '"Pathway"' |
pathwayTitle | Class '"Pathway"' |
pathwayURL | Class '"Pathway"' |
pharmgkb | PharmGKB 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. |
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. |
smpdb | SMPDB pathways |
[-method | Class '"DeprecatedPathwayList"' |
[-method | Class '"PathwayList"' |
[[-method | Class '"DeprecatedPathwayList"' |
[[-method | Class '"PathwayList"' |