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

inst/doc/markowetz-thesis-2006.pdf inst/doc/nem.R inst/doc/nem.pdf vignettes/markowetz-thesis-2006.pdf R/transitive.reduction.R R/dynoNEM_MCMC.R R/nem.bootstrap.R R/transitive.projections.R R/zzz.R R/nem.BN.R R/nem.cont.preprocess.R R/nem.consensus.R R/plotnem.R R/plotEffects.R R/nem.jackknife.R R/transitive.closure.R R/subsets.R R/BN.R R/nem.discretize.R R/SCCgraph.R R/FULLBayesPrior.R R/pairwise.posterior.R R/moduleNetwork.orig.R R/mLL.R R/runMCMC.r R/nem.greedyMAP.R R/generateNetwork.R R/updateHidden.r R/nem.R R/closest.transitive.greedy.R R/DEPN.R R/moduleNetwork.R R/getDensityMatrix.R R/selectEGenes.R R/nem.calcSignificance.R R/plot.nem.R R/FULLmLL.R R/nemModelSelection.R R/print.nem.R R/mcmc.r R/quicknem.R R/sim.intervention.R R/BFSlevel.R R/infer.edge.type.R R/triples.posterior.R R/score.R R/nem.greedy.R R/bum.R R/EMalgo.r R/onestep_mcmc.r R/enumerate.models.R R/local.model.prior.R R/prune.graph.R R/network.AIC.R R/nem.featureselection.R R/additionalFunctions.r man/nem.discretize.Rd man/nem.Rd man/BFSlevel.Rd man/prune.graph.Rd man/subsets.Rd man/BoutrosRNAi2002.Rd man/generateNetwork.Rd man/enumerate.models.Rd man/closest.transitive.greedy.Rd man/internal.Rd man/SahinRNAi2008.Rd man/plotEffects.Rd man/transitive.closure.Rd man/local.model.prior.Rd man/nem.jackknife.Rd man/network.AIC.Rd man/selectEGenes.Rd man/transitive.reduction.Rd man/nem.consensus.Rd man/set.default.parameters.Rd man/getDensityMatrix.Rd man/SCCgraph.Rd man/NiederbergerMediator2012.Rd man/quicknem.Rd man/nemModelSelection.Rd man/nem.bootstrap.Rd man/sim.intervention.Rd man/nem.cont.preprocess.Rd man/Ivanova2006RNAiTimeSeries.Rd man/prior.EgeneAttach.EB.Rd man/transitive.projections.Rd man/infer.edge.type.Rd man/nem.calcSignificance.Rd man/plot.nem.Rd