CellNOptR: Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data.

This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CellNOptR")
AuthorT.Cokelaer, F.Eduati, A.MacNamara, S.Schrier, C.Terfve
Bioconductor views CellBasedAssays CellBiology Proteomics TimeCourse
Date of publicationNone
MaintainerT.Cokelaer <cokelaer@ebi.ac.uk>
LicenseGPL-3
Version1.22.0

View on Bioconductor

Man pages

buildBitString: Build the final bit string vector and times vector based on a...

CellNOptR-package: R version of CellNOptR, boolean features

checkSignals: Check the CNOlist and model matching

CNOdata: Get data from a CellNOpt data repository

CNOlist-class: Class '"CNOlist"'

CNOlistDREAM: Data used for the DREAM3 challenge

CNOlist-methods: List of CNOlist-class methods

CNOlistToy: Toy data

CNOlistToy2: Toy data with 2 time points

CNOlistToyMMB: Toy data

CNORbool: Simple Boolean analysis standalone

CNORwrap: CNOR analysis wrapper

compressModel: Compress a model

computeScoreT1: Compute the score of a model/data set using a bitString to...

computeScoreTN: Compute the score at TN of a model/data set using a bitString...

cSimulator: C-implementation of simulatorT1.

cutAndPlot: Interface to cutAndPlotResults functions.

cutAndPlotResultsT1: Plot the results of an optimisation at t1

cutAndPlotResultsTN: Plot the results of an optimisation at tN

cutCNOlist: Cut a CNOlist structure according to a model

cutModel: Cut a model structure according to a bitstring

cutNONC: Cuts the non-observable/non-controllable species from the...

cutSimList: Cut a simList structure according to a bitstring

defaultParameters: Create a list of default parameters

DreamModel: Model used for the DREAM3 challenge

exhaustive: Exhaustive search over the optimisation of a PKN model on...

expandGates: Expand the gates of a model

findNONC: Find the indexes of the non-observable and non controllable...

gaBinaryT1: Genetic algorithm used to optimise a model

gaBinaryT2: Genetic algorithm for time point 2

gaBinaryTN: Genetic algorithm for time point N

getFit: Compute the score of a model

graph2sif: Convert graph to SIF

indexFinder: Finds the indices, in the model fields, of the species that...

internals: List of CellNOptR internal functions.

makeCNOlist: Make a CNOlist structure

mapBack: Map an optimised model back onto the PKN model.

model2igraph: Convert a model object to a igraph object

model2sif: Convert a model object in sif format

normaliseCNOlist: Normalisation for boolean modelling.

plotCNOlist: Plot the data in a CNOlist

plotCNOlist2: Another version of plotCNOlist that allows to plot 2 cnolist...

plotCNOlistLarge: Plot the data in a CNOlist, for lists with many conditions.

plotCNOlistLargePDF: Plots a CNOlist into a pdf file, for lists with many...

plotCNOlistPDF: Plots a CNOlist into a pdf file.

plotFit: Plot the evolution of an optimisation

plot-methods: plot a '"CNOlist"' object - methods

plotModel: Plot a model

plotOptimResults: Plot the data and simulated values

plotOptimResultsPan: Plots the data and simulated values from any CellNOptR...

plotOptimResultsPDF: Plot the data and simulated values in a pdf file

prep4sim: Prepare a model for simulation

preprocessing: Performs the pre-processing steps

randomizeCNOlist: add noise to the data contained in a CNOlist.

readMIDAS: Reads in a CSV MIDAS file

readSBMLQual: Read a SBMLQual document and returns a SIF object (as...

readSIF: Read a SIF file and create a model object

residualError: Compute the residual error for a dataset

sif2graph: Convert sif to graph

simulateT1: deprecated since version 1.3.28. Cut and simulation of a...

simulateTN: Cut and simulation of a boolean model at t1

simulatorT0: Simulation of a boolean model

simulatorT1: Simulation of a boolean model

simulatorT2: Deprecated since 1.3.28. Use simulateTN function instead....

simulatorTN: Simulation of a boolean model at any time points dependent on...

ToyModel: Toy model

ToyModel2: Toy model

writeDot: Write a model, and attached features, to a dot file

writeMIDAS: Write a CNOlist structure into a MIDAS file

writeNetwork: Write a previous knowledge network model to a sif file (with...

writeReport: Write a report of a CellNOptR analysis

writeScaffold: Writes the scaffold network to a sif file (with attributes)...

writeSIF: Convert a model into a SIF format and save the result in a...

Functions

buildBitString Man page
CellNOptR Man page
CellNOptR-package Man page
checkSignals Man page
CNOdata Man page
CNOlist Man page
CNOlist,ANY Man page
CNOlist-class Man page
CNOlistDREAM Man page
CNOlist-methods Man page
CNOlistToy Man page
CNOlistToy2 Man page
CNOlistToyMMB Man page
CNORbool Man page
CNORwrap Man page
compatCNOlist Man page
compatCNOlist,CNOlist Man page
compatCNOlist,CNOlist,CNOlist-method Man page
compatCNOlist,CNOlist-method Man page
compressModel Man page
computeScoreT1 Man page
computeScoreTN Man page
cSimulator Man page
cutAndPlot Man page
cutAndPlotResultsT1 Man page
cutAndPlotResultsTN Man page
cutCNOlist Man page
cutModel Man page
cutNONC Man page
cutSimList Man page
defaultParameters Man page
DreamModel Man page
exhaustive Man page
expandGates Man page
findNONC Man page
gaBinaryT1 Man page
gaBinaryT2 Man page
gaBinaryTN Man page
getCues Man page
getCues,CNOlist Man page
getCues,CNOlist-method Man page
getFit Man page
getInhibitors Man page
getInhibitors,CNOlist Man page
getInhibitors,CNOlist-method Man page
getInhibitors,CNOlist-method Man page
getSignals Man page
getSignals,CNOlist Man page
getSignals,CNOlist,CNOlist-method Man page
getSignals,CNOlist-method Man page
getStimuli Man page
getStimuli,CNOlist Man page
getStimuli,CNOlist,CNOlist-method Man page
getStimuli,CNOlist-method Man page
getTimepoints Man page
getTimepoints,CNOlist Man page
getTimepoints,CNOlist,CNOlist-method Man page
getTimepoints,CNOlist-method Man page
getVariances Man page
getVariances,CNOlist Man page
getVariances,CNOlist,CNOlist-method Man page
getVariances,CNOlist-method Man page
graph2sif Man page
indexFinder Man page
internals Man page
length Man page
length,CNOlist Man page
length,CNOlist,ANY-method Man page
length,CNOlist-method Man page
makeCNOlist Man page
mapBack Man page
model2igraph Man page
model2sif Man page
normaliseCNOlist Man page
plot Man page
plotCNOlist Man page
plot,CNOlist Man page
plot.CNOlist Man page
plotCNOlist2 Man page
plot,CNOlist,ANY Man page
plot,CNOlist,ANY,CNOlist-method Man page
plot,CNOlist,ANY-method Man page
plot,CNOlist,CNOlist Man page
plot,CNOlist,CNOlist,CNOlist-method Man page
plot,CNOlist,CNOlist,CNOlist-method Man page
plot,CNOlist,CNOlist,CNOlist-method Man page
plot,CNOlist,CNOlist,CNOlist-methods Man page
plot,CNOlist,CNOlist-method Man page
plotCNOlistLarge Man page
plotCNOlistLargePDF Man page
plot,CNOlist-method Man page
plot,CNOlist,missing,CNOlist-method Man page
plot,CNOlist,missing-method Man page
plotCNOlistPDF Man page
plotFit Man page
plotModel Man page
plotOptimResults Man page
plotOptimResultsPan Man page
plotOptimResultsPDF Man page
prep4sim Man page
prep4Sim Man page
preprocessing Man page
randomize Man page
randomizeCNOlist Man page
randomize,CNOlist Man page
randomize,CNOlist,CNOlist-method Man page
randomize,CNOlist-method Man page
readMidas Man page
readMIDAS Man page
readSBMLQual Man page
readSBMLQual Man page
readSif Man page
readSIF Man page
residualError Man page
setSignals<- Man page
setSignals<-,CNOlist Man page
setSignals<-,CNOlist,CNOlist-method Man page
setSignals<-,CNOlist-method Man page
sif2graph Man page
simulateT1 Man page
simulateTN Man page
simulatorT0 Man page
simulatorT1 Man page
simulatorT2 Man page
simulatorTN Man page
ToyModel Man page
ToyModel2 Man page
writeDot Man page
writeMIDAS Man page
writeNetwork Man page
writeReport Man page
writeScaffold Man page
writeSif Man page
writeSIF Man page

Files

.Rinstignore
DESCRIPTION
NAMESPACE
R
R/CNORbool.R R/CNORwrap.R R/CNOdata.R R/CNOlist.R R/CellNOptR-internal.R R/buildBitString.R R/cSimulator.R R/checkSignals.R R/compressModel.R R/computeScoreT1.R R/computeScoreTN.R R/cutAndPlot.R R/cutAndPlotResultsT1.R R/cutAndPlotResultsTN.R R/cutCNOlist.R R/cutModel.R R/cutNONC.R R/cutSimList.R R/defaultParameters.R R/deprecated.R R/exhaustive.R R/expandGates.R R/findNONC.R R/gaBinaryT1.R R/gaBinaryT2.R R/gaBinaryTN.R R/getFit.R R/graph2sif.R R/indexFinder.R R/makeCNOlist.R R/mapBack.R R/model2igraph.R R/model2sif.R R/normaliseCNOlist.R R/plotCNOlist.R R/plotCNOlist2.R R/plotCNOlistLarge.R R/plotCNOlistLargePDF.R R/plotCNOlistPDF.R R/plotFit.R R/plotModel.R R/plotOptimResults.R R/plotOptimResultsPDF.R R/plotOptimResultsPan.R R/prep4sim.R R/preprocessing.R R/rSimulatorT1.R R/randomizeCNOlist.R R/readMIDAS.R R/readSBMLQual.R R/readSIF.R R/residualError.R R/sif2graph.R R/simulateTN.R R/simulatorT0.R R/simulatorT1.R R/simulatorT2.R R/simulatorTN.R R/writeDot.R R/writeMIDAS.R R/writeNetwork.R R/writeReport.R R/writeSIF.R R/writeScaffold.R
build
build/vignette.rds
data
data/CNOlistDREAM.RData
data/CNOlistToy.RData
data/CNOlistToy2.RData
data/CNOlistToyMMB.RData
data/DreamModel.RData
data/ToyModel.RData
data/ToyModel2.RData
inst
inst/DREAMmodel
inst/DREAMmodel/LiverDataDREAMMIDAS.csv
inst/DREAMmodel/LiverPKNDREAM.sif
inst/NEWS.Rd
inst/ToyModel
inst/ToyModel/ToyDataMMB.csv
inst/ToyModel/ToyModelMMB2.sif
inst/ToyModel/ToyPKNMMB.sif
inst/ToyModelT3
inst/ToyModelT3/ToyDataT3.csv
inst/ToyModelT3/ToyModelT3.sif
inst/doc
inst/doc/CellNOptR-vignette.R
inst/doc/CellNOptR-vignette.Rnw
inst/doc/CellNOptR-vignette.pdf
inst/templates
inst/templates/CNOR.css
inst/templates/Rlogo.png
inst/templates/bordercorner.jpg
inst/templates/bordercorner2.jpg
inst/templates/logo_saezrodriguez_mid.gif
inst/templates/phinou.jpeg
man
man/CNORbool.Rd man/CNORwrap.Rd man/CNOdata.Rd man/CNOlist-class.Rd man/CNOlist-methods.Rd man/CNOlistDREAM.Rd man/CNOlistToy.Rd man/CNOlistToy2.Rd man/CNOlistToyMMB.Rd man/CellNOptR-package.Rd man/DreamModel.Rd man/ToyModel.Rd man/ToyModel2.Rd man/buildBitString.Rd man/cSimulator.Rd man/checkSignals.Rd man/compressModel.Rd man/computeScoreT1.Rd man/computeScoreTN.Rd man/cutAndPlot.Rd man/cutAndPlotResultsT1.Rd man/cutAndPlotResultsTN.Rd man/cutCNOlist.Rd man/cutModel.Rd man/cutNONC.Rd man/cutSimList.Rd man/defaultParameters.Rd man/exhaustive.Rd man/expandGates.Rd man/findNONC.Rd man/gaBinaryT1.Rd man/gaBinaryT2.Rd man/gaBinaryTN.Rd man/getFit.Rd man/graph2sif.Rd man/indexFinder.Rd man/internals.Rd man/makeCNOlist.Rd man/mapBack.Rd man/model2igraph.Rd man/model2sif.Rd man/normaliseCNOlist.Rd man/plot-methods.Rd man/plotCNOlist.Rd man/plotCNOlist2.Rd man/plotCNOlistLarge.Rd man/plotCNOlistLargePDF.Rd man/plotCNOlistPDF.Rd man/plotFit.Rd man/plotModel.Rd man/plotOptimResults.Rd man/plotOptimResultsPDF.Rd man/plotOptimResultsPan.Rd man/prep4sim.Rd man/preprocessing.Rd man/randomizeCNOlist.Rd man/readMIDAS.Rd man/readSBMLQual.Rd man/readSIF.Rd man/residualError.Rd man/sif2graph.Rd man/simulateT1.Rd man/simulateTN.Rd man/simulatorT0.Rd man/simulatorT1.Rd man/simulatorT2.Rd man/simulatorTN.Rd man/writeDot.Rd man/writeMIDAS.Rd man/writeNetwork.Rd man/writeReport.Rd man/writeSIF.Rd man/writeScaffold.Rd
src
src/Makevars
src/getFit.c
src/simulatorT1.c
src/simulatorTN.c
tests
tests/test_gaBinaryT1.R tests/test_gaBinaryT2.R tests/test_gaBinaryT3.R tests/test_manySteadyStates.R tests/test_priorBitString.R tests/test_simulateTN.R
vignettes
vignettes/CellNOptR-examples.R
vignettes/CellNOptR-vignette.Rnw
vignettes/CellNOptR0_1flowchart.pdf
vignettes/Fig1.png
vignettes/Fig2.pdf
vignettes/Fig3.pdf
vignettes/Fig4.pdf
vignettes/Fig5.png
vignettes/Fig6.pdf
vignettes/Fig7.pdf
vignettes/Fig8.pdf

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