Man pages for cbg-ethz/pcNEM
Probabilistic combinatorial nested effects model

AdaSimulatedAnnealingAdaptive simulated annealing based inference algorithm
BartonellaRNAiPerturbation with off targets
BFSlevelBuild (generalized) hierarchy by Breath-First Search
BoutrosRNAi2002RNAi data on Drosophila innate immune response
closest.transitive.greedyFind transitively closed graph most similar to the given one
enumerate.modelsExhaustive enumeration of models
generateNetworkRandom networks and data sampling
getDensityMatrixCalculate density matrix from raw p-value matrix
infer.edge.typeInfer regulation direction for each edge
internalinternal functions
Ivanova2006RNAiTimeSeriesPerturbation Time Series
local.model.priorComputes a prior to be used for edge-wise model inference
nemNested Effects Models - main function
nem.bootstrapBootstrapping for nested effect models
nem.calcSignificanceStatistical significance of network hypotheses
nem.consensusStatistically stabile nested effects models
nem.cont.preprocessCalculate classification probabilities of perturbation data...
nem.discretizeDiscretize perturbation data according to control experiments
nem.jackknifeJackknife for nested effect models
nemModelSelectionModel selection for nested effect models
network.AICAIC/BIC criterion for network graph
NiederbergerMediator2012Expression measurements upon perturbation of Mediator...
plotEffectsPlots data according to a phenotypic hierarchy
plot.nemplot nested effect model
prior.EgeneAttach.EBInitialize E-gene attachment prior for empirical Bayes
prune.graphPrunes spurious edges in a phenotypic hierarchy
quicknemQuick run of Nested Effects Models inference
SahinRNAi2008Combinatorial Protein Knockdowns in the ERBB Signaling...
SCCgraphCombines Strongly Connected Components into single nodes
selectEGenesAutomatic selection of most relevant effect reporters
set.default.parametersGet/set hyperparameters
sim.interventionSimulate interventions in a Nested Effects Model
transitive.closureComputes the transitive closure of a directed graph
transitive.projectionsComputes the transitive approximation of a directed graph
transitive.reductionComputes the transitive reduction of a graph
cbg-ethz/pcNEM documentation built on May 23, 2018, 3:30 p.m.