(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies

BFSlevel | Build (generalized) hierarchy by Breath-First Search |

BoutrosRNAi2002 | RNAi data on Drosophila innate immune response |

closest.transitive.greedy | Find transitively closed graph most similar to the given one |

enumerate.models | Exhaustive enumeration of models |

generateNetwork | Random networks and data sampling |

getDensityMatrix | Calculate density matrix from raw p-value matrix |

infer.edge.type | Infer regulation direction for each edge |

internal | internal functions |

Ivanova2006RNAiTimeSeries | Perturbation Time Series |

local.model.prior | Computes a prior to be used for edge-wise model inference |

nem | Nested Effects Models - main function |

nem.bootstrap | Bootstrapping for nested effect models |

nem.calcSignificance | Statistical significance of network hypotheses |

nem.consensus | Statistically stabile nested effects models |

nem.cont.preprocess | Calculate classification probabilities of perturbation data... |

nem.discretize | Discretize perturbation data according to control experiments |

nem.jackknife | Jackknife for nested effect models |

nemModelSelection | Model selection for nested effect models |

network.AIC | AIC/BIC criterion for network graph |

NiederbergerMediator2012 | Expression measurements upon perturbation of Mediator... |

plotEffects | Plots data according to a phenotypic hierarchy |

plot.nem | plot nested effect model |

prior.EgeneAttach.EB | Initialize E-gene attachment prior for empirical Bayes |

prune.graph | Prunes spurious edges in a phenotypic hierarchy |

quicknem | Quick run of Nested Effects Models inference |

SahinRNAi2008 | Combinatorial Protein Knockdowns in the ERBB Signaling... |

SCCgraph | Combines Strongly Connected Components into single nodes |

selectEGenes | Automatic selection of most relevant effect reporters |

set.default.parameters | Get/set hyperparameters |

sim.intervention | Simulate interventions in a Nested Effects Model |

subsets | Subsets |

transitive.closure | Computes the transitive closure of a directed graph |

transitive.projections | Computes the transitive approximation of a directed graph |

transitive.reduction | Computes the transitive reduction of a graph |

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