BFSlevel	BFSlevel
BoutrosRNAi2002	BoutrosRNAi2002
BoutrosRNAiDens	BoutrosRNAi2002
BoutrosRNAiDiscrete	BoutrosRNAi2002
BoutrosRNAiExpression	BoutrosRNAi2002
BoutrosRNAiLods	BoutrosRNAi2002
BoutrosRNAiLogFC	BoutrosRNAi2002
bum.dalt	internal
bum.EM	internal
bum.histogram	internal
bum.mle	internal
bum.negLogLik	internal
bum.palt	internal
bum.qalt	internal
bum.ralt	internal
CheckEdge	transitive.projections
closest.transitive.greedy	closest.transitive.greedy
connectModules	internal
createBN	internal
dat	Ivanova2006RNAiTimeSeries
dat.normalized	SahinRNAi2008
dat.unnormalized	SahinRNAi2008
data.likelihood	internal
dbum	internal
distdecrease	transitive.projections
distincrease	transitive.projections
distincrease1	transitive.projections
distsame	transitive.projections
EdgeEk	transitive.projections
effect.likelihood	internal
encode.interventions	internal
enumerate.models	enumerate.models
enumerate.models2	internal
erase.cycles	internal
exhaustive_BN	internal
filterEGenes	selectEGenes
fit.BN	internal
fitBUM	internal
FourNeighborhood	transitive.projections
FULLmLL	internal
getComponent	internal
getDensityMatrix	getDensityMatrix
getRelevantEGenes	selectEGenes
graychange	internal
infer.edge.type	infer.edge.type
ingreed_BN	internal
internal	internal
inv.logit	internal
is.dag	internal
is.transitive	transitive.projections
Ivanova2006RNAiTimeSeries	Ivanova2006RNAiTimeSeries
learn	internal
learn.conditionals	internal
local.model.prior	local.model.prior
logit	internal
map.int2node	SahinRNAi2008
mLL	internal
moduleNetwork	internal
moduleNetwork.aux	internal
nem	nem
nem.BN	internal
nem.bootstrap	nem.bootstrap
nem.calcSignificance	nem.calcSignificance
nem.consensus	nem.consensus
nem.cont.preprocess	nem.cont.preprocess
nem.discretize	nem.discretize
nem.featureselection	internal
nem.greedy	internal
nem.greedyMAP	internal
nem.jackknife	nem.jackknife
nemModelSelection	nemModelSelection
network.AIC	network.AIC
NiederbergerMediator2012	NiederbergerMediator2012
NiederbergerMediatorLods	NiederbergerMediator2012
NiederbergerMediatorLogFC	NiederbergerMediator2012
NiederbergerMediatorPVals	NiederbergerMediator2012
OneNeighborhood	transitive.projections
optimizecoregraph	internal
optimizemarginal	internal
optimizemarginal.nuInf	internal
pairwise.posterior	internal
parameters_continuous_Bayesian	internal
parameters_continuous_ML	internal
parameters_discrete_Bayesian	internal
parameters_discrete_ML	internal
pbum	internal
PhiDistr	internal
plot.dynoNEM	plot.nem
plot.mc.eminem	plot.nem
plot.ModuleNetwork	plot.nem
plot.nem	plot.nem
plot.nem.BN	plot.nem
plot.nem.bootstrap	plot.nem
plot.nem.consensus	plot.nem
plot.nem.greedy	plot.nem
plot.nem.greedyMAP	plot.nem
plot.nem.jackknife	plot.nem
plot.pairwise	plot.nem
plot.score	plot.nem
plot.triples	plot.nem
plotEffects	plotEffects
plotnem	plot.nem
print.dynoNEM	nem
print.mc.eminem	nem
print.ModuleNetwork	nem
print.nem	nem
print.nem.BN	nem
print.nem.bootstrap	nem.bootstrap
print.nem.consensus	nem.consensus
print.nem.greedy	nem
print.nem.greedyMAP	nem
print.nem.jackknife	nem.jackknife
print.pairwise	nem
print.score	nem
print.triples	nem
prior.EgeneAttach.EB	prior.EgeneAttach.EB
prune.graph	prune.graph
qbum	internal
qqbum	internal
quicknem	quicknem
rbum	internal
remTwoEdges	transitive.projections
SahinRNAi2008	SahinRNAi2008
sample.effect.likelihood	internal
sample.likelihood	internal
sampleData	generateNetwork
sampleData.BN	generateNetwork
sampleRndNetwork	generateNetwork
SCCgraph	SCCgraph
score	internal
score.network	internal
score_BN	internal
score_continuous_Bayesian	internal
score_continuous_ML	internal
score_discrete_Bayesian	internal
score_discrete_ML	internal
selectEGenes	selectEGenes
set.default.parameters	set.default.parameters
sim.intervention	sim.intervention
sim.interventions	internal
subsets	subsets
ThreeNeighborhood	transitive.projections
transitive.closure	transitive.closure
transitive.projections	transitive.projections
transitive.reduction	transitive.reduction
transSubGr	transitive.projections
triples.posterior	internal
TwoNeighborhood	transitive.projections
VecToMat	transitive.projections
which.is.max	internal
