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.

AuthorT.Cokelaer, F.Eduati, A.MacNamara, S.Schrier, C.Terfve
Date of publicationNone
MaintainerT.Cokelaer <cokelaer@ebi.ac.uk>
LicenseGPL-3
Version1.20.0

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...

Files in this package

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

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