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BoolNet (version 2.1.9)

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

2.1.9

License

Artistic-2.0

Maintainer

Hans Kestler

Last Published

October 2nd, 2023

Functions in BoolNet (2.1.9)

attractorsToLaTeX

Create LaTeX state table of attractors

generationFunctions

Generation functions for biologically relevant function classes

generateTimeSeries

Generate time series from a network

binarizeTimeSeries

Binarize a set of real-valued time series

Generate a state vector from single gene values

generateRandomNKNetwork

Generate a random N-K Boolean network

Identify attractors in a Boolean network

getAttractorSequence

Decode the state sequence of a synchronous attractor

Boolean model of the IGF pathway

getTransitionTable

Retrieve the transition table of a network

getStateSummary

Retrieve summary information on a state

loadBioTapestry

Import a network from BioTapestry

getTransitionProbabilities

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

Load a Boolean network from a file

getBasinOfAttraction

Get states in basin of attraction

Visualize state transitions and attractor basins

Load an SBML document

plotPBNTransitions

Visualize the transitions in a probabilistic Boolean network

getPathToAttractor

Get state transitions between a state and its attractor

markovSimulation

Identify important states in probabilistic Boolean networks

print.AttractorInfo

Print attractor cycles

Perturb a Boolean network randomly

perturbTrajectories

Perturb the state trajectories and calculate robustness measures

print.ProbabilisticBooleanNetwork

Print a probabilistic Boolean network

print.SymbolicSimulation

Print simulation results

print.TransitionTable

Print a transition table

simplifyNetwork

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

Plot state tables or transition graphs of attractors

sequenceToLaTeX

Create LaTeX table of state sequences

plotNetworkWiring

Plot the wiring of a Boolean network

yeastTimeSeries

Yeast cell cycle time series data

stateTransition

Perform a transition to the next state

simulateSymbolicModel

Simulate a symbolic Boolean network

symbolicToTruthTable

Convert a symbolic network into a truth table representation

Export a network to SBML

testNetworkProperties

Test properties of networks by comparing them to random networks

reconstructNetwork

Reconstruct a Boolean network from time series of measurements

Plot a sequence of states

Export a network to the Pajek file format

truthTableToSymbolic

Convert a network in truth table representation into a symbolic representation

print.BooleanNetwork

Print a Boolean network

print.MarkovSimulation

Print the results of a Markov chain simulation

Simulate knocked-out or over-expressed genes

Extract a single Boolean network from a probabilistic Boolean network

An artificial probabilistic Boolean network

Mammalian cell cycle network