Construction, Simulation and Analysis of Boolean Networks

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Documentation for package ‘BoolNet’ version 2.1.9

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

attractorsToLaTeX	Create LaTeX state table of attractors
binarizeTimeSeries	Binarize a set of real-valued time series
cellcycle	Mammalian cell cycle network
chooseNetwork	Extract a single Boolean network from a probabilistic Boolean network
examplePBN	An artificial probabilistic Boolean network
fixGenes	Simulate knocked-out or over-expressed genes
generateCanalyzing	Generation functions for biologically relevant function classes
generateNestedCanalyzing	Generation functions for biologically relevant function classes
generateRandomNKNetwork	Generate a random N-K Boolean network
generateState	Generate a state vector from single gene values
generateTimeSeries	Generate time series from a network
getAttractors	Identify attractors in a Boolean network
getAttractorSequence	Decode the state sequence of a synchronous attractor
getBasinOfAttraction	Get states in basin of attraction
getPathToAttractor	Get state transitions between a state and its attractor
getStateSummary	Retrieve summary information on a state
getTransitionProbabilities	Get a matrix of transitions and their probabilities in probabilistic Boolean networks
getTransitionTable	Retrieve the transition table of a network
igf	Boolean model of the IGF pathway
loadBioTapestry	Import a network from BioTapestry
loadNetwork	Load a Boolean network from a file
loadSBML	Load an SBML document
markovSimulation	Identify important states in probabilistic Boolean networks
perturbNetwork	Perturb a Boolean network randomly
perturbTrajectories	Perturb the state trajectories and calculate robustness measures
plotAttractors	Plot state tables or transition graphs of attractors
plotNetworkWiring	Plot the wiring of a Boolean network
plotPBNTransitions	Visualize the transitions in a probabilistic Boolean network
plotSequence	Plot a sequence of states
plotStateGraph	Visualize state transitions and attractor basins
print.AttractorInfo	Print attractor cycles
print.BooleanNetwork	Print a Boolean network
print.BooleanNetworkCollection	Print a probabilistic Boolean network
print.BooleanStateInfo	Print a transition table
print.MarkovSimulation	Print the results of a Markov chain simulation
print.ProbabilisticBooleanNetwork	Print a probabilistic Boolean network
print.SymbolicSimulation	Print simulation results
print.TransitionTable	Print a transition table
reconstructNetwork	Reconstruct a Boolean network from time series of measurements
saveNetwork	Save a network
sequenceToLaTeX	Create LaTeX table of state sequences
sequenceToLaTeX.BooleanNetwork	Create LaTeX table of state sequences
sequenceToLaTeX.data.frame	Create LaTeX table of state sequences
simplifyNetwork	Simplify the functions of a synchronous, asynchronous, or probabilistic Boolean network
simulateSymbolicModel	Simulate a symbolic Boolean network
stateTransition	Perform a transition to the next state
symbolicToTruthTable	Convert a symbolic network into a truth table representation
testAttractorRobustness	Test properties of networks by comparing them to random networks
testIndegree	Test properties of networks by comparing them to random networks
testNetworkProperties	Test properties of networks by comparing them to random networks
testTransitionRobustness	Test properties of networks by comparing them to random networks
toPajek	Export a network to the Pajek file format
toSBML	Export a network to SBML
truthTableToSymbolic	Convert a network in truth table representation into a symbolic representation
yeastTimeSeries	Yeast cell cycle time series data