trena-package	trena-package
.BayesSpikeSolver	BayesSpikeSolver-class
.CandidateFilter	CandidateFilter-class
.EnsembleSolver	EnsembleSolver-class
.FootprintFilter	FootprintFilter-class
.FootprintFinder	FootprintFinder-class
.GeneOntologyFilter	GeneOntologyFilter-class
.HumanDHSFilter	HumanDHSFilter-class
.LassoPVSolver	LassoPVSolver-class
.LassoSolver	LassoSolver-class
.MotifMatcher	MotifMatcher-class
.pcaMax	PCAMax
.PearsonSolver	PearsonSolver-class
.RandomForestSolver	RandomForestSolver-class
.RidgeSolver	RidgeSolver-class
.Solver	Solver-class
.SpearmanSolver	SpearmanSolver-class
.Trena	Trena-class
.VarianceFilter	VarianceFilter-class
.XGBoostSolver	XGBoostSolver-class
addStats	addStats
addStats,PCAMax-method	addStats
addStatsSimple	addStatsSimple
addStatsSimple,PCAMax-method	addStatsSimple
assessSnp	assessSnp
assessSnp,Trena-method	assessSnp
BayesSpikeSolver	BayesSpikeSolver
BayesSpikeSolver-class	BayesSpikeSolver-class
CandidateFilter	CandidateFilter-class
CandidateFilter-class	CandidateFilter-class
closeDatabaseConnections	closeDatabaseConnections
closeDatabaseConnections,FootprintFinder-method	closeDatabaseConnections
createGeneModelFromRegulatoryRegions	createGeneModelFromRegulatoryRegions
createGeneModelFromRegulatoryRegions,Trena-method	createGeneModelFromRegulatoryRegions
createGeneModelFromTfList	createGeneModelFromTfList
createGeneModelFromTfList,Trena-method	createGeneModelFromTfList
elasticNetSolver	elasticNetSolver
EnsembleSolver	EnsembleSolver
EnsembleSolver-class	EnsembleSolver-class
findMatchesByChromosomalRegion	findMatchesByChromosomalRegion
findMatchesByChromosomalRegion,MotifMatcher-method	findMatchesByChromosomalRegion
FootprintFilter	FootprintFilter-class
FootprintFilter-class	FootprintFilter-class
FootprintFinder	FootprintFinder-class
FootprintFinder-class	FootprintFinder-class
GeneOntologyFilter	GeneOntologyFilter-class
GeneOntologyFilter-class	GeneOntologyFilter-class
getAssayData	getAssayData
getAssayData,Solver-method	getAssayData
getAvailableSolvers	getAvailableSolvers
getCandidates	getCandidates
getCandidates,FootprintFilter-method	getCandidates-FootprintFilter-method
getCandidates,GeneOntologyFilter-method	getCandidates-GeneOntologyFilter-method
getCandidates,HumanDHSFilter-method	getCandidates-HumanDHSFilter-method
getCandidates,VarianceFilter-method	getCandidates-VarianceFilter-method
getCandidates-FootprintFilter	getCandidates-FootprintFilter-method
getCandidates-GeneOntologyFilter	getCandidates-GeneOntologyFilter-method
getCandidates-HumanDHSFilter	getCandidates-HumanDHSFilter-method
getCandidates-VarianceFilter	getCandidates-VarianceFilter-method
getChromLoc	getChromLoc
getChromLoc,FootprintFinder-method	getChromLoc
getCoverage	getCoverage
getCoverage,PCAMax-method	getCoverage
getEncodeRegulatoryTableNames	getEncodeRegulatoryTableNames-HumanDHSFilter
getEncodeRegulatoryTableNames,HumanDHSFilter-method	getEncodeRegulatoryTableNames-HumanDHSFilter
getFootprintsForGene	getFootprintsForGene
getFootprintsForGene,FootprintFinder-method	getFootprintsForGene
getFootprintsInRegion	getFootprintsInRegion
getFootprintsInRegion,FootprintFinder-method	getFootprintsInRegion
getGeneModelTableColumnNames	getGeneModelTableColumnNames
getGeneModelTableColumnNames,Trena-method	getGeneModelTableColumnNames
getGenePromoterRegion	getGenePromoterRegion
getGenePromoterRegion,FootprintFinder-method	getGenePromoterRegion
getGtfGeneBioTypes	getGtfGeneBioTypes
getGtfGeneBioTypes,FootprintFinder-method	getGtfGeneBioTypes
getGtfMoleculeTypes	getGtfMoleculeTypes
getGtfMoleculeTypes,FootprintFinder-method	getGtfMoleculeTypes
getPfms	getPfms
getPfms,MotifMatcher-method	getPfms
getPromoterRegionsAllGenes	getPromoterRegionsAllGenes
getPromoterRegionsAllGenes,FootprintFinder-method	getPromoterRegionsAllGenes
getProximalPromoter	getProximalPromoter
getProximalPromoter,Trena-method	getProximalPromoter
getRegulators	getRegulators
getRegulators,Solver-method	getRegulators
getRegulatoryChromosomalRegions	getRegulatoryChromosomalRegions
getRegulatoryChromosomalRegions,Trena-method	getRegulatoryChromosomalRegions
getRegulatoryRegions	getRegulatoryRegions
getRegulatoryRegions,HumanDHSFilter-method	getRegulatoryRegions
getRegulatoryTableColumnNames	getRegulatoryTableColumnNames
getRegulatoryTableColumnNames,Trena-method	getRegulatoryTableColumnNames
getSequence	getSequence
getSequence,MotifMatcher-method	getSequence
getSolverNames	getSolverNames
getSolverNames,EnsembleSolver-method	getSolverNames
getTarget	getTarget
getTarget,Solver-method	getTarget
HumanDHSFilter	HumanDHSFilter-class
HumanDHSFilter-class	HumanDHSFilter-class
LassoPVSolver	LassoPVSolver
LassoPVSolver-class	LassoPVSolver-class
LassoSolver	LassoSolver
LassoSolver-class	LassoSolver-class
MotifMatcher	MotifMatcher-class
MotifMatcher-class	MotifMatcher-class
normalizeModel	normalizeModel
normalizeModel,PCAMax-method	normalizeModel
parseChromLocString	parseChromLocString
parseDatabaseUri	parseDatabaseUri
PCAMax	PCAMax
PearsonSolver	PearsonSolver
PearsonSolver-class	PearsonSolver-class
RandomForestSolver	RandomForestSolver
RandomForestSolver-class	RandomForestSolver-class
rescalePredictorWeights	rescalePredictorWeights
rescalePredictorWeights,Solver-method	rescalePredictorWeights
RidgeSolver	RidgeSolver
RidgeSolver-class	RidgeSolver-class
run	run
run,BayesSpikeSolver-method	solve.BayesSpike
run,EnsembleSolver-method	solve.Ensemble
run,LassoPVSolver-method	solve.LassoPV
run,LassoSolver-method	solve.Lasso
run,PearsonSolver-method	solve.Pearson
run,RandomForestSolver-method	solve.RandomForest
run,RidgeSolver-method	solve.Ridge
run,SpearmanSolver-method	solve.Spearman
run,XGBoostSolver-method	solve.XGBoost
run.BayesSpikeSolver	solve.BayesSpike
run.EnsembleSolver	solve.Ensemble
run.LassoPVSolver	solve.LassoPV
run.LassoSolver	solve.Lasso
run.PearsonSolver	solve.Pearson
run.RandomForestSolver	solve.RandomForest
run.RidgeSolver	solve.Ridge
run.SpearmanSolver	solve.Spearman
run.XGBoostSolver	solve.XGBoost
show,BayesSpikeSolver-method	show.BayesSpikeSolver
show,EnsembleSolver-method	show.EnsembleSolver
show,HumanDHSFilter-method	show-HumanDHSFilter-method
show,LassoPVSolver-method	show.LassoPVSolver
show,LassoSolver-method	show.LassoSolver
show,MotifMatcher-method	show.MotifMatcher
show,PearsonSolver-method	show.PearsonSolver
show,RandomForestSolver-method	show.RandomForestSolver
show,RidgeSolver-method	show.RidgeSolver
show,SpearmanSolver-method	show.SpearmanSolver
show,XGBoostSolver-method	show.XGBoostSolver
show-HumanDHSFilter	show-HumanDHSFilter-method
show.BayesSpikeSolver	show.BayesSpikeSolver
show.EnsembleSolver	show.EnsembleSolver
show.LassoPVSolver	show.LassoPVSolver
show.LassoSolver	show.LassoSolver
show.MotifMatcher	show.MotifMatcher
show.PearsonSolver	show.PearsonSolver
show.RandomForestSolver	show.RandomForestSolver
show.RidgeSolver	show.RidgeSolver
show.SpearmanSolver	show.SpearmanSolver
show.XGBoostSolver	show.XGBoostSolver
solve.BayesSpike	solve.BayesSpike
solve.Ensemble	solve.Ensemble
solve.Lasso	solve.Lasso
solve.LassoPV	solve.LassoPV
solve.Pearson	solve.Pearson
solve.RandomForest	solve.RandomForest
solve.Ridge	solve.Ridge
solve.Spearman	solve.Spearman
solve.XGBoost	solve.XGBoost
Solver	Solver-class
Solver-class	Solver-class
SpearmanSolver	SpearmanSolver
SpearmanSolver-class	SpearmanSolver-class
Trena	Trena-class
Trena-class	Trena-class
VarianceFilter	VarianceFilter-class
VarianceFilter-class	VarianceFilter-class
XGBoostSolver	XGBoostSolver
XGBoostSolver-class	XGBoostSolver-class
