TReNA-package	TReNA-package
.BayesSpikeSolver	BayesSpikeSolver-class
.CandidateFilter	CandidateFilter-class
.EnsembleSolver	EnsembleSolver-class
.FootprintFilter	FootprintFilter-class
.FootprintFinder	FootprintFinder-class
.LassoPVSolver	LassoPVSolver-class
.LassoSolver	LassoSolver-class
.NullFilter	NullFilter-class
.PearsonSolver	PearsonSolver-class
.RandomForestSolver	RandomForestSolver-class
.RidgeSolver	RidgeSolver-class
.Solver	Solver-class
.SpearmanSolver	SpearmanSolver-class
.SqrtLassoSolver	SqrtLassoSolver-class
.TReNA	TReNA-class
.VarianceFilter	VarianceFilter-class
BayesSpikeSolver	BayesSpikeSolver
BayesSpikeSolver-class	BayesSpikeSolver-class
CandidateFilter	CandidateFilter-class
CandidateFilter-class	CandidateFilter-class
closeDatabaseConnections	closeDatabaseConnections
closeDatabaseConnections,FootprintFinder-method	closeDatabaseConnections
EnsembleSolver	EnsembleSolver
EnsembleSolver-class	EnsembleSolver-class
FootprintFilter	FootprintFilter-class
FootprintFilter-class	FootprintFilter-class
FootprintFinder	FootprintFinder-class
FootprintFinder-class	FootprintFinder-class
getAssayData	getAssayData
getAssayData,Solver-method	Solver-class
getCandidates	getCandidates
getCandidates,FootprintFilter-method	getCandidates-FootprintFilter-method
getCandidates,NullFilter-method	getCandidates-NullFilter-method
getCandidates,VarianceFilter-method	getCandidates-VarianceFilter-method
getCandidates-FootprintFilter	getCandidates-FootprintFilter-method
getCandidates-NullFilter	getCandidates-NullFilter-method
getCandidates-VarianceFilter	getCandidates-VarianceFilter-method
getChromLoc	getChromLoc
getChromLoc,FootprintFinder-method	getChromLoc
getFilterAssayData	getFilterAssayData
getFilterAssayData,CandidateFilter-method	CandidateFilter-class
getFootprintsForGene	getFootprintsForGene
getFootprintsForGene,FootprintFinder-method	getFootprintsForGene
getFootprintsInRegion	getFootprintsInRegion
getFootprintsInRegion,FootprintFinder-method	getFootprintsInRegion
getGenePromoterRegion	getGenePromoterRegion
getGenePromoterRegion,FootprintFinder-method	getGenePromoterRegion
getGtfGeneBioTypes	getGtfGeneBioTypes
getGtfGeneBioTypes,FootprintFinder-method	getGtfGeneBioTypes
getGtfMoleculeTypes	getGtfMoleculeTypes
getGtfMoleculeTypes,FootprintFinder-method	getGtfMoleculeTypes
getPromoterRegionsAllGenes	getPromoterRegionsAllGenes
getPromoterRegionsAllGenes,FootprintFinder-method	getPromoterRegionsAllGenes
getSolverName	getSolverName
getSolverName,TReNA-method	TReNA-class
getSolverObject	getSolverObject
getSolverObject,TReNA-method	TReNA-class
LassoPVSolver	LassoPVSolver
LassoPVSolver-class	LassoPVSolver-class
LassoSolver	LassoSolver
LassoSolver-class	LassoSolver-class
mapMotifsToTFsMergeIntoTable	mapMotifsToTFsMergeIntoTable
mapMotifsToTFsMergeIntoTable,FootprintFinder-method	mapMotifsToTFsMergeIntoTable
NullFilter	NullFilter-class
NullFilter-class	NullFilter-class
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,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,SqrtLassoSolver-method	solve.SqrtLasso
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.SqrtLassoSolver	solve.SqrtLasso
solve	solve
solve,TReNA-method	solve
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.SqrtLasso	solve.SqrtLasso
solve.TReNA	solve
Solver	Solver-class
Solver-class	Solver-class
SpearmanSolver	SpearmanSolver
SpearmanSolver-class	SpearmanSolver-class
SqrtLassoSolver	SqrtLassoSolver
SqrtLassoSolver-class	SqrtLassoSolver-class
TReNA	TReNA-class
TReNA-class	TReNA-class
VarianceFilter	VarianceFilter-class
VarianceFilter-class	VarianceFilter-class
