R version of CellNOpt, boolean features only

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Documentation for package ‘CellNOptR’ version 1.2.0

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CellNOptR-package R version of CellNOptR, boolean features
CellNOptR R version of CellNOptR, boolean features
checkSignals Check the CNOlist and model matching
CNOlistDREAM Data used for the DREAM3 challenge
CNOlistToy Toy data
CNOlistToy2 Toy data with 2 time points
CNORwrap CNOR analysis wrapper
compressModel Compress a model
cutAndPlotResultsT1 Plot the results of an optimisation at t1
cutAndPlotResultsT2 Plot the results of an optimisation at t2
cutNONC Cuts the non-observable/non-controllable species off the model
cutSimList Cut a simList structure according to a bitstring
defaultParameters Create a list of default parameters
DreamModel Model used for the DREAM3 challenge
expandGates Expand the gates of a model
findNONC Find the indexes of the non-observable and non controllable species
gaBinaryT1 Genetic algorithm used to optimise a model
gaBinaryT2 Genetic algorithm for time point 2
getFit Compute the score of a model
indexFinder Finds the indices, in the Model fields, of the species that are measured/inhibited/stimulated
makeCNOlist Make a CNOlist structure
normaliseCNOlist Normalisation for boolean modelling.
plotCNOlist Plot the data in a 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 conditions.
plotCNOlistPDF Plots a CNOlist into a pdf file.
plotFit Plot the evolution of an optimisation
plotModel Plot a model
plotOptimResults Plot the data and simulated values
plotOptimResultsPDF Plot the data and simulated values in a pdf file
prep4Sim Prepare a model for simulation
preprocessing Performs the pre-processing steps
readMIDAS Reads in a csv MIDAS file
readSif Read a sif file and create a model object
residualError Compute the residual error for a dataset
simulateT1 Cut and simulation of a boolean model at t1
simulatorT1 Simulation of a boolean model
simulatorT2 Simulation of a boolean model for time 2
ToyModel Toy model
ToyModel2 Toy model
writeDot Write a model, and attached features, to a dot file
writeNetwork Write a previous knowledge network model to a sif file (with attribute files), as well as a dot file
writeReport Write a report of a CellNOptR analysis
writeScaffold Writes the scaffold network to a sif file (with attributes) and to a dot file