Generation, reconstruction, simulation and analysis of synchronous, asynchronous, and probabilistic Boolean networks

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Documentation for package ‘BoolNet’ version 1.61

Help Pages

BoolNet-package Analyze Boolean networks
attractorsToLaTeX Create LaTeX state table of attractors
binarizeTimeSeries Binarize a set of real-valued time series
BoolNet Analyze Boolean networks
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
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
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
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.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
stateTransition Perform a transition to the next state
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
toPajek Export a network to the Pajek file format
toSBML Export a network to SBML
yeastTimeSeries Yeast cell cycle time series data