CellNOptR-package	CellNOptR-package
buildBitString	buildBitString
CellNOptR	CellNOptR-package
checkSignals	checkSignals
CNOdata	CNOdata
CNOlist	CNOlist-class
CNOlist-class	CNOlist-class
CNOlist-methods	CNOlist-methods
CNOlistDREAM	CNOlistDREAM
CNOlistToy	CNOlistToy
CNOlistToy2	CNOlistToy2
CNOlistToyMMB	CNOlistToyMMB
CNORbool	CNORbool
CNORwrap	CNORwrap
compatCNOlist	CNOlist-methods
compatCNOlist,CNOlist	CNOlist-methods
compatCNOlist,CNOlist-method	CNOlist-class
compressModel	compressModel
computeScoreT1	computeScoreT1
computeScoreTN	computeScoreTN
cSimulator	cSimulator
cutAndPlot	cutAndPlot
cutAndPlotResultsT1	cutAndPlotResultsT1
cutAndPlotResultsTN	cutAndPlotResultsTN
cutCNOlist	cutCNOlist
cutModel	cutModel
cutNONC	cutNONC
cutSimList	cutSimList
defaultParameters	defaultParameters
DreamModel	DreamModel
exhaustive	exhaustive
expandGates	expandGates
findNONC	findNONC
gaBinaryT1	gaBinaryT1
gaBinaryT2	gaBinaryT2
gaBinaryTN	gaBinaryTN
getCues	CNOlist-methods
getCues,CNOlist	CNOlist-methods
getCues,CNOlist-method	CNOlist-class
getFit	getFit
getInhibitors	CNOlist-methods
getInhibitors,CNOlist	CNOlist-methods
getInhibitors,CNOlist-method	CNOlist-class
getSignals	CNOlist-methods
getSignals,CNOlist	CNOlist-methods
getSignals,CNOlist-method	CNOlist-class
getStimuli	CNOlist-methods
getStimuli,CNOlist	CNOlist-methods
getStimuli,CNOlist-method	CNOlist-class
getTimepoints	CNOlist-methods
getTimepoints,CNOlist	CNOlist-methods
getTimepoints,CNOlist-method	CNOlist-class
getVariances	CNOlist-methods
getVariances,CNOlist	CNOlist-methods
getVariances,CNOlist,CNOlist-method	CNOlist-methods
getVariances,CNOlist-method	CNOlist-class
graph2sif	graph2sif
indexFinder	indexFinder
internals	internals
length	CNOlist-methods
length,CNOlist	CNOlist-methods
length,CNOlist,ANY-method	CNOlist-methods
length,CNOlist-method	CNOlist-class
makeCNOlist	makeCNOlist
mapBack	mapBack
model2igraph	model2igraph
model2sif	model2sif
normaliseCNOlist	normaliseCNOlist
plot,CNOlist,ANY-method	plot-methods
plot,CNOlist,CNOlist,CNOlist-method	CNOlist-methods
plot,CNOlist,CNOlist-method	CNOlist-class
plot.CNOlist	plot-methods
plotCNOlist	plotCNOlist
plotCNOlist2	plotCNOlist2
plotCNOlistLarge	plotCNOlistLarge
plotCNOlistLargePDF	plotCNOlistLargePDF
plotCNOlistPDF	plotCNOlistPDF
plotFit	plotFit
plotModel	plotModel
plotOptimResults	plotOptimResults
plotOptimResultsPan	plotOptimResultsPan
plotOptimResultsPDF	plotOptimResultsPDF
prep4Sim	prep4sim
prep4sim	prep4sim
preprocessing	preprocessing
randomize	CNOlist-methods
randomize,CNOlist	CNOlist-methods
randomize,CNOlist,CNOlist-method	CNOlist-methods
randomize,CNOlist-method	CNOlist-class
randomizeCNOlist	randomizeCNOlist
readMIDAS	readMIDAS
readMidas	readMIDAS
readSBMLQual	readSBMLQual
readSIF	readSIF
readSif	readSIF
residualError	residualError
setSignals<-	CNOlist-methods
setSignals<-,CNOlist	CNOlist-methods
setSignals<-,CNOlist,CNOlist-method	CNOlist-methods
setSignals<-,CNOlist-method	CNOlist-class
sif2graph	sif2graph
simulateT1	simulateT1
simulateTN	simulateTN
simulatorT0	simulatorT0
simulatorT1	simulatorT1
simulatorT2	simulatorT2
simulatorTN	simulatorTN
ToyModel	ToyModel
ToyModel2	ToyModel2
writeDot	writeDot
writeMIDAS	writeMIDAS
writeNetwork	writeNetwork
writeReport	writeReport
writeScaffold	writeScaffold
writeSIF	writeSIF
writeSif	writeSIF
