Man pages for saezlab/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...
build_sif_table_from_ruleBuild a SIF table from a logic rule written in a string
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.
plotAnnotatedModelplots network graph with highlighted edges. plots the graph...
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.
readBNDRead network from BND file
readBNETRead network from BNET file
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...
saezlab/CellNOptR documentation built on Nov. 11, 2019, 2:03 p.m.