Provides methods to reconstruct and generate synchronous, asynchronous, probabilistic and temporal Boolean networks, and to analyze and visualize attractors in Boolean networks.
|Author||Christoph Müssel [aut], Martin Hopfensitz [aut], Dao Zhou [aut], Hans A. Kestler [aut, cre], Armin Biere [ctb] (contributed PicoSAT code), Troy D. Hanson [ctb] (contributed uthash macros)|
|Date of publication||2016-11-21 12:23:47|
|Maintainer||Hans A. Kestler <firstname.lastname@example.org>|
attractorsToLaTeX: Create LaTeX state table of attractors
binarizeTimeSeries: Binarize a set of real-valued time series
BoolNet-package: Construction, Simulation and Analysis of Boolean Networks
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