API for trena
Fit transcriptional regulatory networks using gene expression, priors, machine learning

Global functions
.BayesSpikeSolver Man page
.CandidateFilter Man page
.EnsembleSolver Man page
.FootprintFilter Man page
.FootprintFinder Man page
.GeneOntologyFilter Man page
.HumanDHSFilter Man page
.LassoPVSolver Man page
.LassoSolver Man page
.MotifMatcher Man page
.PearsonSolver Man page
.RandomForestSolver Man page
.RidgeSolver Man page
.Solver Man page
.SpearmanSolver Man page
.SqrtLassoSolver Man page
.Trena Man page
.VarianceFilter Man page
BayesSpikeSolver Man page Source code
BayesSpikeSolver-class Man page
CandidateFilter Man page Man page Source code
CandidateFilter-class Man page
EnsembleSolver Man page Source code
EnsembleSolver-class Man page
FootprintFilter Man page Man page Source code
FootprintFilter-class Man page
FootprintFinder Man page Man page Source code
FootprintFinder-class Man page Man page
GeneOntologyFilter Man page Man page Source code
GeneOntologyFilter-class Man page
HumanDHSFilter Man page Man page Source code
HumanDHSFilter-class Man page
LassoPVSolver Man page Source code
LassoPVSolver-class Man page
LassoSolver Man page Source code
LassoSolver-class Man page
MotifMatcher Man page Man page Source code
MotifMatcher-class Man page Man page
PearsonSolver Man page Source code
PearsonSolver-class Man page
RandomForestSolver Man page Source code
RandomForestSolver-class Man page
RidgeSolver Man page Source code
RidgeSolver-class Man page
Solver Man page Man page Source code
Solver-class Man page
SpearmanSolver Man page Source code
SpearmanSolver-class Man page
SqrtLassoSolver Man page Source code
SqrtLassoSolver-class Man page
Trena Man page Man page Source code
Trena-class Man page
VarianceFilter Man page Man page Source code
VarianceFilter-class Man page
addEnsembleScores Source code
assessSnp Man page
assessSnp,Trena-method Man page
callFootprintFilter Source code
callHumanDHSFilter Source code
closeDatabaseConnections Man page
closeDatabaseConnections,FootprintFinder-method Man page
createGeneModel Man page
createGeneModel,Trena-method Man page
elasticNetSolver Source code
findMatchesByChromosomalRegion Man page
findMatchesByChromosomalRegion,MotifMatcher-method Man page
findMotifs Source code
getAssayData Man page
getAssayData,Solver-method Man page
getAvailableSolvers Man page Source code
getCandidates Man page
getCandidates,FootprintFilter-method Man page
getCandidates,GeneOntologyFilter-method Man page
getCandidates,HumanDHSFilter-method Man page
getCandidates,VarianceFilter-method Man page
getCandidates-FootprintFilter Man page
getCandidates-GeneOntologyFilter Man page
getCandidates-HumanDHSFilter Man page
getCandidates-VarianceFilter Man page
getChromLoc Man page
getChromLoc,FootprintFinder-method Man page
getEncodeRegulatoryTableNames Man page
getEncodeRegulatoryTableNames,HumanDHSFilter-method Man page
getFootprintsForGene Man page
getFootprintsForGene,FootprintFinder-method Man page
getFootprintsInRegion Man page
getFootprintsInRegion,FootprintFinder-method Man page
getGeneModelTableColumnNames Man page
getGeneModelTableColumnNames,Trena-method Man page
getGenePromoterRegion Man page
getGenePromoterRegion,FootprintFinder-method Man page
getGtfGeneBioTypes Man page
getGtfGeneBioTypes,FootprintFinder-method Man page
getGtfMoleculeTypes Man page
getGtfMoleculeTypes,FootprintFinder-method Man page
getPfms Man page
getPfms,MotifMatcher-method Man page
getPromoterRegionsAllGenes Man page
getPromoterRegionsAllGenes,FootprintFinder-method Man page
getProximalPromoter Man page
getProximalPromoter,Trena-method Man page
getRegulators Man page
getRegulators,Solver-method Man page
getRegulatoryChromosomalRegions Man page
getRegulatoryChromosomalRegions,Trena-method Man page
getRegulatoryRegions Man page
getRegulatoryRegions,HumanDHSFilter-method Man page
getRegulatoryTableColumnNames Man page
getRegulatoryTableColumnNames,Trena-method Man page
getScoredMotifs Source code
getSequence Man page
getSequence,MotifMatcher-method Man page
getSolverNames Man page
getSolverNames,EnsembleSolver-method Man page
getTarget Man page
getTarget,Solver-method Man page
matchPwmForwardAndReverse Source code
njectSnp Source code
parseChromLocString Man page Source code
parseDatabaseUri Man page Source code
parseJasparPwm Source code
parseLine Source code
printf Source code Source code Source code Source code Source code Source code Source code
readRawJasparMatrices Source code
rescalePredictorWeights Man page
rescalePredictorWeights,Solver-method Man page
run Man page
run,BayesSpikeSolver-method Man page
run,EnsembleSolver-method Man page
run,LassoPVSolver-method Man page
run,LassoSolver-method Man page
run,PearsonSolver-method Man page
run,RandomForestSolver-method Man page
run,RidgeSolver-method Man page
run,SpearmanSolver-method Man page
run,SqrtLassoSolver-method Man page
run.BayesSpikeSolver Man page
run.EnsembleSolver Man page
run.LassoPVSolver Man page
run.LassoSolver Man page
run.PearsonSolver Man page
run.RandomForestSolver Man page
run.RidgeSolver Man page
run.SpearmanSolver Man page
run.SqrtLassoSolver Man page
show,BayesSpikeSolver-method Man page
show,EnsembleSolver-method Man page
show,HumanDHSFilter-method Man page
show,LassoPVSolver-method Man page
show,LassoSolver-method Man page
show,MotifMatcher-method Man page
show,PearsonSolver-method Man page
show,RandomForestSolver-method Man page
show,RidgeSolver-method Man page
show,SpearmanSolver-method Man page
show,SqrtLassoSolver-method Man page
show-HumanDHSFilter Man page
show.BayesSpikeSolver Man page
show.EnsembleSolver Man page
show.LassoPVSolver Man page
show.LassoSolver Man page
show.MotifMatcher Man page
show.PearsonSolver Man page
show.RandomForestSolver Man page
show.RidgeSolver Man page
show.SpearmanSolver Man page
show.SqrtLassoSolver Man page
solve.BayesSpike Man page
solve.Ensemble Man page
solve.Lasso Man page
solve.LassoPV Man page
solve.Pearson Man page
solve.RandomForest Man page
solve.Ridge Man page
solve.Spearman Man page
solve.SqrtLasso Man page
trena-package Man page
trena documentation built on March 18, 2018, 2:33 p.m.