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.

Author
T.Cokelaer, F.Eduati, A.MacNamara, S.Schrier, C.Terfve
Date of publication
None
Maintainer
T.Cokelaer <cokelaer@ebi.ac.uk>
License
GPL-3
Version
1.20.0

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