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 |