Index

B

BLEval (class in BLEval) (module) BLEval.computeAUC (module) BLEval.computeDGAUC (module) BLEval.computeEarlyPrec (module) BLEval.computeJaccard (module) BLEval.computeNetMotifs (module) BLEval.computeSignedEPrec (module) BLEval.computeSpearman (module) BLEval.parseTime (module) BLPlot (module) BLPlot.CuratedOverview (module) BLPlot.NetworkMotifs (module) BLRun (class in BLRun) (module)

BLRun.genie3Runner (module) BLRun.grisliRunner (module) BLRun.grnboost2Runner (module) BLRun.grnvbemRunner (module) BLRun.jump3Runner (module) BLRun.leapRunner (module) BLRun.pidcRunner (module) BLRun.ppcorRunner (module) BLRun.runner (module) BLRun.scingeRunner (module) BLRun.scnsRunner (module) BLRun.scodeRunner (module) BLRun.scribeRunner (module) BLRun.sinceritiesRunner (module)

C

computeAUC() (BLEval.BLEval method) computeEarlyPrec() (BLEval.BLEval method) computeJaccard() (BLEval.BLEval method) computeNetMotifs() (BLEval.BLEval method) computePairwiseJacc() (in module BLEval.computeJaccard)

computeScores() (in module BLEval.computeAUC) (in module BLEval.computeDGAUC) computeSignedEPrec() (BLEval.BLEval method) computeSpearman() (BLEval.BLEval method) ConfigParser (class in BLEval) (class in BLRun)

D

deltaW() (in module src.simulator)

E

EarlyPrec() (in module BLEval.computeEarlyPrec) eulersde() (in module src.simulator)

execute_runners() (BLRun.BLRun method) Experiment() (in module src.BoolODE)

G

generateInputFiles() (in module src.utils) generateInputs() (BLRun.runner.Runner method) (in module BLRun.genie3Runner) (in module BLRun.grisliRunner) (in module BLRun.grnboost2Runner) (in module BLRun.grnvbemRunner) (in module BLRun.jump3Runner) (in module BLRun.leapRunner) (in module BLRun.pidcRunner) (in module BLRun.ppcorRunner) (in module BLRun.scingeRunner) (in module BLRun.scnsRunner) (in module BLRun.scodeRunner) (in module BLRun.scribeRunner) (in module BLRun.sinceritiesRunner)

generateModelDict() (in module src.BoolODE) get_ss() (in module src.utils) getInitialCondition() (in module src.BoolODE) getNetProp() (in module BLEval.computeNetMotifs) getParameters() (in module src.BoolODE) getSaneNval() (in module src.utils) getTime() (in module BLEval.parseTime)

I

InputSettings (class in BLEval) (class in BLRun)

J

Jaccard() (in module BLEval.computeJaccard)

M

main() (in module src.BoolODE)

minmaxnorm() (in module src.utils) Motifs() (in module BLEval.computeNetMotifs)

N

noise() (in module src.simulator)

normalizeData() (in module src.utils) normalizeExp() (in module src.utils)

O

OutputSettings (class in BLEval) (class in BLRun)

P

parse() (BLEval.ConfigParser static method) (BLRun.ConfigParser static method) parse_time_files() (in module BLEval.parseTime) parseArgs() (in module src.BoolODE) parseOutput() (BLRun.runner.Runner method) (in module BLRun.genie3Runner) (in module BLRun.grisliRunner) (in module BLRun.grnboost2Runner) (in module BLRun.grnvbemRunner) (in module BLRun.jump3Runner) (in module BLRun.leapRunner) (in module BLRun.pidcRunner) (in module BLRun.ppcorRunner) (in module BLRun.scingeRunner) (in module BLRun.scnsRunner) (in module BLRun.scodeRunner) (in module BLRun.scribeRunner) (in module BLRun.sinceritiesRunner)

parseTime() (BLEval.BLEval method) plot() (in module BLPlot.CuratedOverview) (in module BLPlot.NetworkMotifs) PRROC() (in module BLEval.computeAUC) (in module BLEval.computeDGAUC)

R

readBooleanRules() (in module src.BoolODE) run() (BLRun.runner.Runner method) (in module BLRun.genie3Runner) (in module BLRun.grisliRunner) (in module BLRun.grnboost2Runner) (in module BLRun.grnvbemRunner) (in module BLRun.jump3Runner) (in module BLRun.leapRunner) (in module BLRun.pidcRunner) (in module BLRun.ppcorRunner) (in module BLRun.scingeRunner) (in module BLRun.scnsRunner) (in module BLRun.scodeRunner) (in module BLRun.scribeRunner) (in module BLRun.sinceritiesRunner)

Runner (class in BLRun.runner)

S

sampleCellFromTraj() (in module src.utils) sampleTimeSeries() (in module src.utils) signedEPrec() (in module BLEval.computeSignedEPrec) simulateAndSample() (in module src.BoolODE) simulateModel() (in module src.BoolODE)

Spearman() (in module BLEval.computeSpearman) src (module) src.BoolODE (module) src.simulator (module) src.utils (module)

W

writeModelToFile() (in module src.utils)

writeParametersToFile() (in module src.utils)