Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology

dBUMfit | Function to fit a p-value distribution under beta-uniform... |

dBUMscore | Function to transform p-values into scores according to the... |

dCheckParallel | Function to check whether parallel computing should be used... |

dCommSignif | Function to test the significance of communities within a... |

dContrast | Function to help build the contrast matrix |

dDAGancestor | Function to find common ancestors of two terms/nodes from a... |

dDAGannotate | Function to generate a subgraph of a direct acyclic graph... |

dDAGgeneSim | Function to calculate pair-wise semantic similarity between... |

dDAGinduce | Function to generate a subgraph of a direct acyclic graph... |

dDAGlevel | Function to define/calculate the level of nodes in a direct... |

dDAGreverse | Function to reverse the edge direction of a direct acyclic... |

dDAGroot | Function to find the root node of a direct acyclic graph... |

dDAGtermSim | Function to calculate pair-wise semantic similarity between... |

dDAGtip | Function to find the tip node(s) of a direct acyclic graph... |

dEnricher | Function to conduct enrichment analysis given the input data... |

dEnricherView | Function to view enrichment results of dEnricher |

dFDRscore | Function to transform fdr into scores according to... |

dFunArgs | Function to assign (and evaluate) arguments with default... |

dGSEA | Function to conduct gene set enrichment analysis given the... |

dGSEAview | Function to view enrichment results in a sample-specific... |

dGSEAwrite | Function to write out enrichment results |

dNetConfidence | Function to append the confidence information from the source... |

dNetFind | Function to find heuristically maximum scoring subgraph |

dNetInduce | Function to generate a subgraph induced by given vertices and... |

dNetPipeline | Function to setup the pipeline for finding maximum-scoring... |

dNetReorder | Function to reorder the multiple graph colorings within a... |

dPvalAggregate | Function to aggregate p values |

dRDataLoader | Function to load dnet built-in RData |

dRWR | Function to implement Random Walk with Restart (RWR) on the... |

dRWRcontact | Function to estimate RWR-based contact strength between... |

dRWRpipeline | Function to setup a pipeine to estimate RWR-based contact... |

dSVDsignif | Function to obtain SVD-based gene significance from the input... |

ig.HPPA | Human Phenotype Phenotypic Abnormality (HPPA). |

org.Hs.egHPPA | Annotations of Human Entrez Genes (EG) by Human Phenotype... |

visBoxplotAdv | Function to visualise a data frame using advanced boxplot |

visDAG | Function to visualise a direct acyclic graph (DAG) with node... |

visGSEA | Function to visualise running enrichment score for a given... |

visNet | Function to visualise a graph object of class "igraph" or... |

visNetAnimate | Function to animate the same graph but with multiple graph... |

visNetArc | Function to visualise an igraph object via arc diagram |

visNetCircle | Function to visualise an igraph object via circle diagram |

visNetMul | Function to visualise the same graph but with multiple graph... |

visNetReorder | Function to visualise the multiple graph colorings reorded... |

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