Man pages for CellNOptR
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

buildBitStringBuild the final bit string vector and times vector based on a...
CellNOptR-packageR version of CellNOptR, boolean features
checkSignalsCheck the CNOlist and model matching
CNOdataGet data from a CellNOpt data repository
CNOlist-classClass '"CNOlist"'
CNOlistDREAMData used for the DREAM3 challenge
CNOlist-methodsList of CNOlist-class methods
CNOlistToyToy data
CNOlistToy2Toy data with 2 time points
CNOlistToyMMBToy data
CNORboolSimple Boolean analysis standalone
CNORwrapCNOR analysis wrapper
compressModelCompress a model
computeScoreT1Compute the score of a model/data set using a bitString to...
computeScoreTNCompute the score at TN of a model/data set using a bitString...
crossInhibitedDataIf an inhibitor is also a measured species, replace the data...
cSimulatorC-implementation of simulatorT1.
cutAndPlotInterface to cutAndPlotResults functions.
cutAndPlotResultsT1Plot the results of an optimisation at t1
cutAndPlotResultsTNPlot the results of an optimisation at tN
cutCNOlistCut a CNOlist structure according to a model
cutModelCut a model structure according to a bitstring
cutNONCCuts the non-observable/non-controllable species from the...
cutSimListCut a simList structure according to a bitstring
defaultParametersCreate a list of default parameters
DreamModelModel used for the DREAM3 challenge
exhaustiveExhaustive search over the optimisation of a PKN model on...
expandGatesExpand the gates of a model
findNONCFind the indexes of the non-observable and non controllable...
gaBinaryT1Genetic algorithm used to optimise a model
gaBinaryT2Genetic algorithm for time point 2
gaBinaryTNGenetic algorithm for time point N
getFitCompute the score of a model
graph2sifConvert graph to SIF
indexFinderFinds the indices, in the model fields, of the species that...
internalsList of CellNOptR internal functions.
makeCNOlistMake a CNOlist structure
mapBackMap an optimised model back onto the PKN model.
model2igraphConvert a model object to a igraph object
model2sifConvert a model object in sif format
normaliseCNOlistNormalisation for boolean modelling.
plotCNOlistPlot the data in a CNOlist
plotCNOlist2Another version of plotCNOlist that allows to plot 2 cnolist...
plotCNOlistLargePlot the data in a CNOlist, for lists with many conditions.
plotCNOlistLargePDFPlots a CNOlist into a pdf file, for lists with many...
plotCNOlistPDFPlots a CNOlist into a pdf file.
plotFitPlot the evolution of an optimisation
plot-methodsplot a '"CNOlist"' object - methods
plotModelPlot a model
plotOptimResultsPlot the data and simulated values
plotOptimResultsPanPlots the data and simulated values from any CellNOptR...
plotOptimResultsPDFPlot the data and simulated values in a pdf file
prep4simPrepare a model for simulation
preprocessingPerforms the pre-processing steps
randomizeCNOlistadd noise to the data contained in a CNOlist.
readMIDASReads in a CSV MIDAS file
readSBMLQualRead a SBMLQual document and returns a SIF object (as...
readSIFRead a SIF file and create a model object
residualErrorCompute the residual error for a dataset
sif2graphConvert sif to graph
simulateT1deprecated since version 1.3.28. Cut and simulation of a...
simulateTNCut and simulation of a boolean model at t1
simulatorT0Simulation of a boolean model
simulatorT1Simulation of a boolean model
simulatorT2Deprecated since 1.3.28. Use simulateTN function instead....
simulatorTNSimulation of a boolean model at any time points dependent on...
toSBMLExport the network to SBML-qual format
ToyModelToy model
ToyModel2Toy model
writeDotWrite a model, and attached features, to a dot file
writeMIDASWrite a CNOlist structure into a MIDAS file
writeNetworkWrite a previous knowledge network model to a sif file (with...
writeReportWrite a report of a CellNOptR analysis
writeScaffoldWrites the scaffold network to a sif file (with attributes)...
writeSIFConvert a model into a SIF format and save the result in a...
CellNOptR documentation built on Jan. 5, 2019, 7:04 p.m.