CellNOptR-package | R version of CellNOptR, boolean features |
CellNOptR | R version of CellNOptR, boolean features |
checkSignals | Check the CNOlist and model matching |
CNOdata | Get data from a CellNOpt data repository |
CNOlist | Class '"CNOlist"' |
CNOlist-class | Class '"CNOlist"' |
CNOlist-methods | List of CNOlist-class methods |
CNOlistDREAM | Data used for the DREAM3 challenge |
CNOlistToy | Toy data |
CNOlistToy2 | Toy data with 2 time points |
CNORbool | Simple Boolean analysis standalone |
CNORwrap | CNOR analysis wrapper |
compatCNOlist | List of CNOlist-class methods |
compatCNOlist,CNOlist | List of CNOlist-class methods |
compatCNOlist-method | Class '"CNOlist"' |
compressModel | Compress a model |
computeScoreT1 | Compute the score of a model/data set using a bitString to cut the model. |
computeScoreTN | Compute the score at TN of a model/data set using a bitString to cut the model. |
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 model |
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 MIDAS data. |
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 |
gaBinaryTN | Genetic algorithm for time point N |
getCues | List of CNOlist-class methods |
getCues,CNOlist | List of CNOlist-class methods |
getCues-method | Class '"CNOlist"' |
getFit | Compute the score of a model |
getInhibitors | List of CNOlist-class methods |
getInhibitors,CNOlist | List of CNOlist-class methods |
getInhibitors-method | Class '"CNOlist"' |
getSignals | List of CNOlist-class methods |
getSignals,CNOlist | List of CNOlist-class methods |
getSignals-method | Class '"CNOlist"' |
getStimuli | List of CNOlist-class methods |
getStimuli,CNOlist | List of CNOlist-class methods |
getStimuli-method | Class '"CNOlist"' |
getTimepoints | List of CNOlist-class methods |
getTimepoints,CNOlist | List of CNOlist-class methods |
getTimepoints-method | Class '"CNOlist"' |
getVariances | List of CNOlist-class methods |
getVariances,CNOlist | List of CNOlist-class methods |
getVariances-method | Class '"CNOlist"' |
getVariances-method | List of CNOlist-class methods |
graph2sif | Convert graph to SIF |
indexFinder | Finds the indices, in the model fields, of the species that are measured/inhibited/stimulated |
internals | List of CellNOptR internal functions. |
length | List of CNOlist-class methods |
length,CNOlist | List of CNOlist-class methods |
length-method | Class '"CNOlist"' |
length-method | List of CNOlist-class methods |
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. |
plot-method | Class '"CNOlist"' |
plot-method | List of CNOlist-class methods |
plot-method | plot a '"CNOlist"' object - methods |
plot.CNOlist | plot a '"CNOlist"' object - methods |
plotCNOlist | Plot the data in a CNOlist |
plotCNOlist2 | Another version of plotCNOlist that allows to plot 2 cnolist in the same layout to compare them. This function uses ggplot2 library. It is recommended for small data sets (about 15 species). |
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 |
plotOptimResultsPan | Plots the data and simulated values from any CellNOptR formalism |
plotOptimResultsPDF | Plot the data and simulated values in a pdf file |
prep4Sim | Prepare a model for simulation |
prep4sim | Prepare a model for simulation |
preprocessing | Performs the pre-processing steps |
randomize | List of CNOlist-class methods |
randomize,CNOlist | List of CNOlist-class methods |
randomize-method | Class '"CNOlist"' |
randomize-method | List of CNOlist-class methods |
randomizeCNOlist | add noise to the data contained in a CNOlist. |
readMIDAS | Reads in a CSV MIDAS file |
readMidas | Reads in a CSV MIDAS file |
readSBMLQual | Read a SBMLQual document and returns a SIF object (as returned by readSIG |
readSIF | Read a SIF file and create a model object |
readSif | Read a SIF file and create a model object |
residualError | Compute the residual error for a dataset |
setSignals<- | List of CNOlist-class methods |
setSignals<-,CNOlist | List of CNOlist-class methods |
setSignals<--method | Class '"CNOlist"' |
setSignals<--method | List of CNOlist-class methods |
sif2graph | Convert sif to graph |
simulateTN | Cut and simulation of a boolean model at t1 |
simulatorT0 | Simulation of a boolean model |
simulatorT1 | Simulation of a boolean model |
simulatorTN | Simulation of a boolean model at any time points dependent on a previous one. |
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 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 |
writeSIF | Convert a model into a SIF format and save the result in a file. |
writeSif | Convert a model into a SIF format and save the result in a file. |