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B C D E F G I L M N O P Q R S T V W
| BFSlevel | Build (generalized) hierarchy by Breath-First Search |
| BoutrosRNAi2002 | RNAi data on Drosophila innate immune response |
| BoutrosRNAiDens | RNAi data on Drosophila innate immune response |
| BoutrosRNAiDiscrete | RNAi data on Drosophila innate immune response |
| BoutrosRNAiExpression | RNAi data on Drosophila innate immune response |
| BoutrosRNAiLods | RNAi data on Drosophila innate immune response |
| BoutrosRNAiLogFC | RNAi data on Drosophila innate immune response |
| bum.dalt | internal functions |
| bum.EM | internal functions |
| bum.histogram | internal functions |
| bum.mle | internal functions |
| bum.negLogLik | internal functions |
| bum.palt | internal functions |
| bum.qalt | internal functions |
| bum.ralt | internal functions |
| CheckEdge | Computes the transitive approximation of a directed graph |
| closest.transitive.greedy | Find transitively closed graph most similar to the given one |
| connectModules | internal functions |
| createBN | internal functions |
| dat | Perturbation Time Series |
| dat.normalized | Combinatorial Protein Knockdowns in the ERBB Signaling Pathway |
| dat.unnormalized | Combinatorial Protein Knockdowns in the ERBB Signaling Pathway |
| data.likelihood | internal functions |
| dbum | internal functions |
| distdecrease | Computes the transitive approximation of a directed graph |
| distincrease | Computes the transitive approximation of a directed graph |
| distincrease1 | Computes the transitive approximation of a directed graph |
| distsame | Computes the transitive approximation of a directed graph |
| EdgeEk | Computes the transitive approximation of a directed graph |
| effect.likelihood | internal functions |
| encode.interventions | internal functions |
| enumerate.models | Exhaustive enumeration of models |
| enumerate.models2 | internal functions |
| erase.cycles | internal functions |
| exhaustive_BN | internal functions |
| filterEGenes | Automatic selection of most relevant effect reporters |
| fit.BN | internal functions |
| fitBUM | internal functions |
| FourNeighborhood | Computes the transitive approximation of a directed graph |
| FULLmLL | internal functions |
| getComponent | internal functions |
| getDensityMatrix | Calculate density matrix from raw p-value matrix |
| getRelevantEGenes | Automatic selection of most relevant effect reporters |
| graychange | internal functions |
| infer.edge.type | Infer regulation direction for each edge |
| ingreed_BN | internal functions |
| internal | internal functions |
| inv.logit | internal functions |
| is.dag | internal functions |
| is.transitive | Computes the transitive approximation of a directed graph |
| Ivanova2006RNAiTimeSeries | Perturbation Time Series |
| learn | internal functions |
| learn.conditionals | internal functions |
| local.model.prior | Computes a prior to be used for edge-wise model inference |
| logit | internal functions |
| map.int2node | Combinatorial Protein Knockdowns in the ERBB Signaling Pathway |
| mLL | internal functions |
| moduleNetwork | internal functions |
| moduleNetwork.aux | internal functions |
| nem | Nested Effects Models - main function |
| nem.BN | internal functions |
| 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 according to control experiments |
| nem.discretize | Discretize perturbation data according to control experiments |
| nem.featureselection | internal functions |
| nem.greedy | internal functions |
| nem.greedyMAP | internal functions |
| 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 subunits |
| NiederbergerMediatorLods | Expression measurements upon perturbation of Mediator subunits |
| NiederbergerMediatorLogFC | Expression measurements upon perturbation of Mediator subunits |
| NiederbergerMediatorPVals | Expression measurements upon perturbation of Mediator subunits |
| OneNeighborhood | Computes the transitive approximation of a directed graph |
| optimizecoregraph | internal functions |
| optimizemarginal | internal functions |
| optimizemarginal.nuInf | internal functions |
| pairwise.posterior | internal functions |
| parameters_continuous_Bayesian | internal functions |
| parameters_continuous_ML | internal functions |
| parameters_discrete_Bayesian | internal functions |
| parameters_discrete_ML | internal functions |
| pbum | internal functions |
| PhiDistr | internal functions |
| plot.dynoNEM | plot nested effect model |
| plot.mc.eminem | plot nested effect model |
| plot.ModuleNetwork | plot nested effect model |
| plot.nem | plot nested effect model |
| plot.nem.BN | plot nested effect model |
| plot.nem.bootstrap | plot nested effect model |
| plot.nem.consensus | plot nested effect model |
| plot.nem.greedy | plot nested effect model |
| plot.nem.greedyMAP | plot nested effect model |
| plot.nem.jackknife | plot nested effect model |
| plot.pairwise | plot nested effect model |
| plot.score | plot nested effect model |
| plot.triples | plot nested effect model |
| plotEffects | Plots data according to a phenotypic hierarchy |
| plotnem | plot nested effect model |
| print.dynoNEM | Nested Effects Models - main function |
| print.mc.eminem | Nested Effects Models - main function |
| print.ModuleNetwork | Nested Effects Models - main function |
| print.nem | Nested Effects Models - main function |
| print.nem.BN | Nested Effects Models - main function |
| print.nem.bootstrap | Bootstrapping for nested effect models |
| print.nem.consensus | Statistically stabile nested effects models |
| print.nem.greedy | Nested Effects Models - main function |
| print.nem.greedyMAP | Nested Effects Models - main function |
| print.nem.jackknife | Jackknife for nested effect models |
| print.pairwise | Nested Effects Models - main function |
| print.score | Nested Effects Models - main function |
| print.triples | Nested Effects Models - main function |
| prior.EgeneAttach.EB | Initialize E-gene attachment prior for empirical Bayes |
| prune.graph | Prunes spurious edges in a phenotypic hierarchy |
| qbum | internal functions |
| qqbum | internal functions |
| quicknem | Quick run of Nested Effects Models inference |
| rbum | internal functions |
| remTwoEdges | Computes the transitive approximation of a directed graph |
| SahinRNAi2008 | Combinatorial Protein Knockdowns in the ERBB Signaling Pathway |
| sample.effect.likelihood | internal functions |
| sample.likelihood | internal functions |
| sampleData | Random networks and data sampling |
| sampleData.BN | Random networks and data sampling |
| sampleRndNetwork | Random networks and data sampling |
| SCCgraph | Combines Strongly Connected Components into single nodes |
| score | internal functions |
| score.network | internal functions |
| score_BN | internal functions |
| score_continuous_Bayesian | internal functions |
| score_continuous_ML | internal functions |
| score_discrete_Bayesian | internal functions |
| score_discrete_ML | internal functions |
| selectEGenes | Automatic selection of most relevant effect reporters |
| set.default.parameters | Get/set hyperparameters |
| sim.intervention | Simulate interventions in a Nested Effects Model |
| sim.interventions | internal functions |
| subsets | Subsets |
| ThreeNeighborhood | Computes the transitive approximation of a directed graph |
| 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 |
| transSubGr | Computes the transitive approximation of a directed graph |
| triples.posterior | internal functions |
| TwoNeighborhood | Computes the transitive approximation of a directed graph |
| VecToMat | Computes the transitive approximation of a directed graph |
| which.is.max | internal functions |