BFSlevel                Build (generalized) hierarchy by Breath-First
                        Search
BoutrosRNAi2002         RNAi data on Drosophila innate immune response
Ivanova2006RNAiTimeSeries
                        Perturbation Time Series
NiederbergerMediator2012
                        Expression measurements upon perturbation of
                        Mediator subunits
SCCgraph                Combines Strongly Connected Components into
                        single nodes
SahinRNAi2008           Combinatorial Protein Knockdowns in the ERBB
                        Signaling Pathway
closest.transitive.greedy
                        Find transitively closed graph most similar to
                        the given one
enumerate.models        Exhaustive enumeration of models
getDensityMatrix        Calculate density matrix from raw p-value
                        matrix
getRelevantEGenes       Automatic selection of most relevant effect
                        reporters
infer.edge.type         Infer regulation direction for each edge
internal                internal functions
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 according to control
                        experiments
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
plot.nem                plot nested effect model
plotEffects             Plots data according to a phenotypic hierarchy
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
sampleRndNetwork        Random networks and data sampling
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
