GRAPH Interaction from pathway Topological Environment

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. |

cytoscapePlot | Plot a pathway graph in Cytoscape |

DeprecatedPathwayList-class | Class '"DeprecatedPathwayList"' |

humancyc | Humancyc pathways |

kegg | KEGG pathways |

nci | NCI pathways |

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"' |

prepareSPIA | Prepare pathway dataset needed by runSPIA. |

reactome | Reactome pathways |

runClipper | Run a topological analysis on an expression dataset using... |

runClipperMulti | Run a topological analysis on an expression dataset using... |

runDEGraph | Run a topological analysis on an expression dataset using... |

runDEGraphMulti | Run a topological analysis on an expression dataset using... |

runSPIA | Run SPIA analysis |

runTopologyGSA | Run a topological analysis on an expression dataset using... |

runTopologyGSAMulti | Run a topological analysis on an expression dataset using... |

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