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BoolNet (version 2.1.8)

Construction, Simulation and Analysis of Boolean Networks

Description

Functions to reconstruct, generate, and simulate synchronous, asynchronous, probabilistic, and temporal Boolean networks. Provides also functions to analyze and visualize attractors in Boolean networks .

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Version

Install

install.packages('BoolNet')

Monthly Downloads

894

Version

2.1.8

License

Artistic-2.0

Maintainer

Hans Kestler

Last Published

February 27th, 2023

Functions in BoolNet (2.1.8)

cellcycle

Mammalian cell cycle network
attractorsToLaTeX

Create LaTeX state table of attractors
generateRandomNKNetwork

Generate a random N-K Boolean network
binarizeTimeSeries

Binarize a set of real-valued time series
generateState

Generate a state vector from single gene values
fixGenes

Simulate knocked-out or over-expressed genes
generateTimeSeries

Generate time series from a network
BoolNet-package

Construction, Simulation and Analysis of Boolean Networks
getBasinOfAttraction

Get states in basin of attraction
getStateSummary

Retrieve summary information on a state
getTransitionProbabilities

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

Import a network from BioTapestry
chooseNetwork

Extract a single Boolean network from a probabilistic Boolean network
examplePBN

An artificial probabilistic Boolean network
getAttractorSequence

Decode the state sequence of a synchronous attractor
generationFunctions

Generation functions for biologically relevant function classes
getAttractors

Identify attractors in a Boolean network
igf

Boolean model of the IGF pathway
getTransitionTable

Retrieve the transition table of a network
getPathToAttractor

Get state transitions between a state and its attractor
loadNetwork

Load a Boolean network from a file
plotNetworkWiring

Plot the wiring of a Boolean network
perturbTrajectories

Perturb the state trajectories and calculate robustness measures
plotSequence

Plot a sequence of states
plotStateGraph

Visualize state transitions and attractor basins
perturbNetwork

Perturb a Boolean network randomly
markovSimulation

Identify important states in probabilistic Boolean networks
plotPBNTransitions

Visualize the transitions in a probabilistic Boolean network
reconstructNetwork

Reconstruct a Boolean network from time series of measurements
saveNetwork

Save a network
print.TransitionTable

Print a transition table
print.SymbolicSimulation

Print simulation results
loadSBML

Load an SBML document
print.BooleanNetwork

Print a Boolean network
print.AttractorInfo

Print attractor cycles
print.ProbabilisticBooleanNetwork

Print a probabilistic Boolean network
print.MarkovSimulation

Print the results of a Markov chain simulation
plotAttractors

Plot state tables or transition graphs of attractors
yeastTimeSeries

Yeast cell cycle time series data
sequenceToLaTeX

Create LaTeX table of state sequences
truthTableToSymbolic

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

Simulate a symbolic Boolean network
simplifyNetwork

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

Export a network to the Pajek file format
stateTransition

Perform a transition to the next state
toSBML

Export a network to SBML
symbolicToTruthTable

Convert a symbolic network into a truth table representation
testNetworkProperties

Test properties of networks by comparing them to random networks