/usr/lib/R/site-library/BoolNet/INDEX is in r-cran-boolnet 2.1.3-2.
This file is owned by root:root, with mode 0o644.
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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 network
examplePBN An artificial probabilistic Boolean network
fixGenes Simulate knocked-out or over-expressed genes
generateCanalyzing 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
getAttractorSequence Decode the state sequence of a synchronous
attractor
getAttractors Identify attractors in a Boolean network
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.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
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
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
truthTableToSymbolic Convert a network in truth table representation
into a symbolic representation
yeastTimeSeries Yeast cell cycle time series data
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