# R version of CellNOpt, boolean features only

## Documentation for package ‘CellNOptR’ version 1.0.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

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
CNORwrap | CNOR analysis wrapper
compressModel | Compress a model
cutAndPlotResultsT1 | Plot the results of an optimisation at t1
cutNONC | Cuts the non-observable/non-controllable species off the model
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
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
plotOptimResults | Plot the data and simulated values
plotOptimResultsPDF | Plot the data and simulated values in a pdf file
prep4Sim | Prepare a model for simulation
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
ToyModel | Toy mode
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