nem: (Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies
Version 2.50.0

The package 'nem' allows to reconstruct features of pathways from the nested structure of perturbation effects. It takes as input (1.) a set of pathway components, which were perturbed, and (2.) phenotypic readout of these perturbations (e.g. gene expression, protein expression). The output is a directed graph representing the phenotypic hierarchy.

AuthorHolger Froehlich, Florian Markowetz, Achim Tresch, Theresa Niederberger, Christian Bender, Matthias Maneck, Claudio Lottaz, Tim Beissbarth
Bioconductor views Bioinformatics GraphsAndNetworks Microarray NetworkInference Pathways SystemsBiology
Date of publicationNone
MaintainerHolger Froehlich <frohlich@bit.uni-bonn.de>
LicenseGPL (>= 2)
Version2.50.0
URL http://www.bioconductor.org
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("nem")

Popular man pages

BoutrosRNAi2002: RNAi data on Drosophila innate immune response
internal: internal functions
nem: Nested Effects Models - main function
network.AIC: AIC/BIC criterion for network graph
plot.nem: plot nested effect model
transitive.closure: Computes the transitive closure of a directed graph
transitive.reduction: Computes the transitive reduction of a graph
See all...

All man pages Function index File listing

Man pages

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

Functions

BFSlevel Man page Source code
BoutrosRNAi2002 Man page
BoutrosRNAiDens Man page
BoutrosRNAiDiscrete Man page
BoutrosRNAiExpression Man page
BoutrosRNAiLods Man page
BoutrosRNAiLogFC Man page
CheckEdge Man page
EMforMCMC Source code
EdgeEk Man page Source code
FULLmLL Man page Source code
FourNeighborhood Man page Source code
Ivanova2006RNAiTimeSeries Man page
NiederbergerMediator2012 Man page
NiederbergerMediatorLods Man page
NiederbergerMediatorLogFC Man page
NiederbergerMediatorPVals Man page
OneNeighborhood Man page Source code
PhiDistr Man page Source code
SCCgraph Man page Source code
SahinRNAi2008 Man page
ThreeNeighborhood Man page Source code
TwoNeighborhood Man page Source code
VecToMat Man page Source code
bum.EM Man page Source code
bum.dalt Man page Source code
bum.histogram Man page Source code
bum.mle Man page Source code
bum.negLogLik Man page Source code
bum.palt Man page Source code
bum.qalt Man page Source code
bum.ralt Man page Source code
calcLikelihood Source code
calculateHiddenPrior Source code
closest.transitive.greedy Man page Source code
connectModules Man page
connectModules.aux Source code
connectModules.orig Source code
connectModules2 Source code
createBN Man page Source code
dat Man page
dat.normalized Man page
dat.unnormalized Man page
data.likelihood Man page Source code
dbum Man page Source code
distdecrease Man page Source code
distincrease Man page Source code
distincrease1 Man page Source code
distsame Man page Source code
dynoNEM.perturb Source code
dynoNEM.posteriorEGenePos Source code
dynoNEM_MCMC Source code
effect.likelihood Man page Source code
encode.interventions Man page Source code
enumerate.models Man page Source code
enumerate.models2 Man page Source code
erase.cycles Man page Source code
exhaustive_BN Man page Source code
filterEGenes Man page Source code
final_attachement Source code
fit.BN Man page Source code
fitBUM Man page Source code
get.deletions Source code
get.insertions Source code
get.reversions Source code
getComponent Man page Source code
getDensityMatrix Man page Source code
getFinalTheta Source code
getRelevantEGenes Man page Source code
graychange Man page
infer.edge.type Man page Source code
ingreed_BN Man page Source code
internal Man page
inv.logit Man page Source code
is.dag Man page Source code
is.transitive Man page Source code
learn Man page Source code
learn.conditionals Man page Source code
local.model.prior Man page Source code
logit Man page Source code
mLL Man page Source code
map.int2node Man page
mcmc Source code
moduleNetwork Man page Source code
moduleNetwork.aux Man page Source code
moduleNetwork.orig Source code
nem Man page Source code
nem.BN Man page Source code
nem.bootstrap Man page Source code
nem.bootstrap.list Source code
nem.calcSignificance Man page Source code
nem.consensus Man page Source code
nem.cont.preprocess Man page Source code
nem.discretize Man page Source code
nem.featureselection Man page Source code
nem.greedy Man page Source code
nem.greedyMAP Man page Source code
nem.jackknife Man page Source code
nemModelSelection Man page Source code
network.AIC Man page Source code
onLoad Source code
onestep_EMiNEM Source code
onestep_mcmc Source code
optimizecoregraph Man page Source code
optimizemarginal Man page Source code
optimizemarginal.nuInf Man page Source code
pairwise.posterior Man page Source code
parameters_continuous_Bayesian Man page
parameters_continuous_ML Man page
parameters_discrete_Bayesian Man page
parameters_discrete_ML Man page
pbum Man page Source code
plot.ModuleNetwork Man page Source code
plot.dynoNEM Man page Source code
plot.mc.eminem Man page Source code
plot.nem Man page Source code
plot.nem.BN Man page Source code
plot.nem.bootstrap Man page Source code
plot.nem.consensus Man page Source code
plot.nem.greedy Man page Source code
plot.nem.greedyMAP Man page Source code
plot.nem.jackknife Man page Source code
plot.pairwise Man page Source code
plot.score Man page Source code
plot.score.list Source code
plot.triples Man page Source code
plotEffects Man page Source code
plotnem Man page Source code
print.ModuleNetwork Man page Source code
print.dynoNEM Man page Source code
print.mc.eminem Man page Source code
print.nem Man page Source code
print.nem.BN Man page Source code
print.nem.bootstrap Man page Source code
print.nem.consensus Man page Source code
print.nem.greedy Man page Source code
print.nem.greedyMAP Man page Source code
print.nem.jackknife Man page Source code
print.pairwise Man page Source code
print.score Man page Source code
print.score.list Source code
print.triples Man page Source code
prior.EgeneAttach.EB Man page Source code
prune.graph Man page Source code
qbum Man page Source code
qqbum Man page Source code
quicknem Man page Source code
rbum Man page Source code
remTwoEdges Man page Source code
runMCMC Source code
sample.effect.likelihood Man page Source code
sample.likelihood Man page Source code
sampleData Man page Source code
sampleData.BN Man page
sampleRndNetwork Man page Source code
score Man page Source code
score.aux Source code
score.network Man page Source code
score_BN Man page Source code
score_continuous_Bayesian Man page Source code
score_continuous_ML Man page Source code
score_discrete_Bayesian Man page Source code
score_discrete_ML Man page Source code
selectEGenes Man page
set.default.parameters Man page Source code
sim.intervention Man page Man page Source code
sim.interventions Man page Source code
subsets Man page Source code
transSubGr Man page Source code
transitive.closure Man page Source code
transitive.projections Man page Source code
transitive.reduction Man page Source code
triples.posterior Man page Source code
updateHidden Source code
which.is.max Man page

Files

DESCRIPTION
NAMESPACE
R
R/BFSlevel.R
R/BN.R
R/DEPN.R
R/EMalgo.r
R/FULLBayesPrior.R
R/FULLmLL.R
R/SCCgraph.R
R/additionalFunctions.r
R/bum.R
R/closest.transitive.greedy.R
R/dynoNEM_MCMC.R
R/enumerate.models.R
R/generateNetwork.R
R/getDensityMatrix.R
R/infer.edge.type.R
R/local.model.prior.R
R/mLL.R
R/mcmc.r
R/moduleNetwork.R
R/moduleNetwork.orig.R
R/nem.BN.R
R/nem.R
R/nem.bootstrap.R
R/nem.calcSignificance.R
R/nem.consensus.R
R/nem.cont.preprocess.R
R/nem.discretize.R
R/nem.featureselection.R
R/nem.greedy.R
R/nem.greedyMAP.R
R/nem.jackknife.R
R/nemModelSelection.R
R/network.AIC.R
R/onestep_mcmc.r
R/pairwise.posterior.R
R/plot.nem.R
R/plotEffects.R
R/plotnem.R
R/print.nem.R
R/prune.graph.R
R/quicknem.R
R/runMCMC.r
R/score.R
R/selectEGenes.R
R/sim.intervention.R
R/subsets.R
R/transitive.closure.R
R/transitive.projections.R
R/transitive.reduction.R
R/triples.posterior.R
R/updateHidden.r
R/zzz.R
build
build/vignette.rds
data
data/BoutrosRNAi2002.RData
data/Ivanova2006RNAiTimeSeries.RData
data/NiederbergerMediator2012.RData
data/SahinRNAi2008.RData
data/datalist
inst
inst/doc
inst/doc/ModuleNetworks1.png
inst/doc/markowetz-thesis-2006.pdf
inst/doc/nem.R
inst/doc/nem.Rnw
inst/doc/nem.pdf
inst/doc/references.bib
man
man/BFSlevel.Rd
man/BoutrosRNAi2002.Rd
man/Ivanova2006RNAiTimeSeries.Rd
man/NiederbergerMediator2012.Rd
man/SCCgraph.Rd
man/SahinRNAi2008.Rd
man/closest.transitive.greedy.Rd
man/enumerate.models.Rd
man/generateNetwork.Rd
man/getDensityMatrix.Rd
man/infer.edge.type.Rd
man/internal.Rd
man/local.model.prior.Rd
man/nem.Rd
man/nem.bootstrap.Rd
man/nem.calcSignificance.Rd
man/nem.consensus.Rd
man/nem.cont.preprocess.Rd
man/nem.discretize.Rd
man/nem.jackknife.Rd
man/nemModelSelection.Rd
man/network.AIC.Rd
man/plot.nem.Rd
man/plotEffects.Rd
man/prior.EgeneAttach.EB.Rd
man/prune.graph.Rd
man/quicknem.Rd
man/selectEGenes.Rd
man/set.default.parameters.Rd
man/sim.intervention.Rd
man/subsets.Rd
man/transitive.closure.Rd
man/transitive.projections.Rd
man/transitive.reduction.Rd
src
src/MCMC.c
src/netlearn.c
src/netlearn.h
src/wrapper.c
vignettes
vignettes/ModuleNetworks1.png
vignettes/markowetz-thesis-2006.pdf
vignettes/nem.Rnw
vignettes/references.bib
nem documentation built on May 20, 2017, 10:44 p.m.

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