Index

A

add_genes_to_network() (in module BNMPy.build_bn_from_kg)

B

BNMPy.BMatrix module BNMPy.booleanNetwork module BNMPy.build_bn_from_kg module

BNMPy.PBN module BNMPy.steady_state module BooleanNetwork (class in BNMPy.booleanNetwork) buildK() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method)

C

compute_stationary_deterministic() (BNMPy.steady_state.SteadyStateCalculator method) compute_stationary_mc() (BNMPy.steady_state.SteadyStateCalculator method)

compute_stationary_tsmc() (BNMPy.steady_state.SteadyStateCalculator method) compute_steady_state() (BNMPy.steady_state.SteadyStateCalculator method) copy() (BNMPy.PBN.ProbabilisticBN method)

G

get_convergence_info() (BNMPy.steady_state.SteadyStateCalculator method) get_upstream_genes() (in module BNMPy.BMatrix) getBias() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method) getDataFromFile() (in module BNMPy.booleanNetwork) getMaxConnectivity() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method) getMeanConnectivity() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method)

getParametersFromFile() (in module BNMPy.booleanNetwork) getRandomInitialNodeValues() (in module BNMPy.booleanNetwork) getRandomParameters() (in module BNMPy.booleanNetwork) getRealization() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method) getTrajectory() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method)

I

initializeOutput() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method)

K

knockdown() (BNMPy.PBN.ProbabilisticBN method)

knockout() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method)

L

load_network_from_file() (in module BNMPy.BMatrix) load_network_from_string() (in module BNMPy.BMatrix)

load_pbn_from_file() (in module BNMPy.BMatrix) load_pbn_from_string() (in module BNMPy.BMatrix) load_signor_network() (in module BNMPy.build_bn_from_kg)

M

merge_network() (in module BNMPy.build_bn_from_kg) module BNMPy.BMatrix BNMPy.booleanNetwork BNMPy.build_bn_from_kg BNMPy.PBN BNMPy.steady_state

P

ProbabilisticBN (class in BNMPy.PBN)

R

rename_nodes() (in module BNMPy.BMatrix)

reset_network_conditions() (BNMPy.steady_state.SteadyStateCalculator method)

S

set_experimental_conditions() (BNMPy.steady_state.SteadyStateCalculator method) setInitialValue() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method) setInitialValues() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method)

stateToWrite() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method) SteadyStateCalculator (class in BNMPy.steady_state)

T

toGraph() (BNMPy.booleanNetwork.BooleanNetwork method)

U

undoKnockouts() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method) update() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method)

update_cumulative_probabilities() (BNMPy.PBN.ProbabilisticBN method) update_noise() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method) updateUntilAttractorIsReached() (BNMPy.booleanNetwork.BooleanNetwork method)

W

writeNetworkHistory() (BNMPy.booleanNetwork.BooleanNetwork method) (BNMPy.PBN.ProbabilisticBN method)