R: Construction, Simulation and Analysis of Boolean Networks

# Construction, Simulation and Analysis of Boolean Networks

## Documentation for package ‘BoolNet’ version 2.1.4

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

## Help Pages

BoolNet-package | Construction, Simulation and Analysis of Boolean Networks
attractorsToLaTeX | Create LaTeX state table of attractors
binarizeTimeSeries | Binarize a set of real-valued time series
BoolNet | Construction, Simulation and Analysis of 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
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