Man pages for BoolNet
Construction, Simulation and Analysis of Boolean Networks
| 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... |
| 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 |
| generationFunctions | Generation functions for biologically relevant function... |
| 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... |
| 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... |
| 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.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... |
| saveNetwork | Save a network |
| sequenceToLaTeX | Create LaTeX table of state sequences |
| simplifyNetwork | Simplify the functions of a synchronous, asynchronous, or... |
| simulateSymbolicModel | Simulate a symbolic Boolean network |
| stateTransition | Perform a transition to the next state |
| symbolicToTruthTable | Convert a symbolic network into a truth table representation |
| testNetworkProperties | Test properties of networks by comparing them to random... |
| 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... |
| yeastTimeSeries | Yeast cell cycle time series data |
