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BoolNet (version 2.1.5)

Construction, Simulation and Analysis of Boolean Networks

Description

Provides methods to reconstruct and generate synchronous, asynchronous, probabilistic and temporal Boolean networks, and to analyze and visualize attractors in Boolean networks.

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Version

Install

install.packages('BoolNet')

Monthly Downloads

894

Version

2.1.5

License

Artistic-2.0

Maintainer

Hans Kestler

Last Published

April 16th, 2019

Functions in BoolNet (2.1.5)

chooseNetwork

Extract a single Boolean network from a probabilistic Boolean network
generateState

Generate a state vector from single gene values
generateTimeSeries

Generate time series from a network
examplePBN

An artificial probabilistic Boolean network
generateRandomNKNetwork

Generate a random N-K Boolean network
fixGenes

Simulate knocked-out or over-expressed genes
getAttractors

Identify attractors in a Boolean network
getBasinOfAttraction

Get states in basin of attraction
getPathToAttractor

Get state transitions between a state and its attractor
perturbTrajectories

Perturb the state trajectories and calculate robustness measures
getTransitionProbabilities

Get a matrix of transitions and their probabilities in probabilistic Boolean networks
igf

Boolean model of the IGF pathway
loadBioTapestry

Import a network from BioTapestry
getTransitionTable

Retrieve the transition table of a network
binarizeTimeSeries

Binarize a set of real-valued time series
cellcycle

Mammalian cell cycle network
markovSimulation

Identify important states in probabilistic Boolean networks
perturbNetwork

Perturb a Boolean network randomly
getStateSummary

Retrieve summary information on a state
plotNetworkWiring

Plot the wiring of a Boolean network
plotSequence

Plot a sequence of states
generationFunctions

Generation functions for biologically relevant function classes
plotStateGraph

Visualize state transitions and attractor basins
getAttractorSequence

Decode the state sequence of a synchronous attractor
print.SymbolicSimulation

Print simulation results
plotAttractors

Plot state tables or transition graphs of attractors
plotPBNTransitions

Visualize the transitions in a probabilistic Boolean network
print.AttractorInfo

Print attractor cycles
print.MarkovSimulation

Print the results of a Markov chain simulation
reconstructNetwork

Reconstruct a Boolean network from time series of measurements
symbolicToTruthTable

Convert a symbolic network into a truth table representation
testNetworkProperties

Test properties of networks by comparing them to random networks
print.ProbabilisticBooleanNetwork

Print a probabilistic Boolean network
print.BooleanNetwork

Print a Boolean network
BoolNet-package

Construction, Simulation and Analysis of Boolean Networks
attractorsToLaTeX

Create LaTeX state table of attractors
saveNetwork

Save a network
simulateSymbolicModel

Simulate a symbolic Boolean network
print.TransitionTable

Print a transition table
truthTableToSymbolic

Convert a network in truth table representation into a symbolic representation
yeastTimeSeries

Yeast cell cycle time series data
stateTransition

Perform a transition to the next state
toPajek

Export a network to the Pajek file format
sequenceToLaTeX

Create LaTeX table of state sequences
simplifyNetwork

Simplify the functions of a synchronous, asynchronous, or probabilistic Boolean network
loadSBML

Load an SBML document
loadNetwork

Load a Boolean network from a file
toSBML

Export a network to SBML