Uses of Package
de.jstacs.motifDiscovery

Packages that use de.jstacs.motifDiscovery

de.jstacs.motifDiscovery	This package provides the framework including the interface for any de novo motif discoverer.
de.jstacs.sequenceScores.statisticalModels.differentiable	Provides all DifferentiableStatisticalModels, which can compute the gradient with respect to their parameters for a given input Sequence.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels	Provides DifferentiableStatisticalModels that are directed graphical models.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture	Provides DifferentiableSequenceScores that are mixtures of other DifferentiableSequenceScores.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif

Classes in de.jstacs.motifDiscovery used by de.jstacs.motifDiscovery

MotifDiscoverer
This is the interface that any tool for de-novo motif discovery should implement.

MotifDiscoverer.KindOfProfile
This enum can be used to determine which kind of profile should be returned.

MotifDiscovererToolBox
This class contains static methods for the MotifDiscoverer.

MutableMotifDiscoverer
This is the interface that any tool for de-novo motif discovery should implement that allows any modify-operations like shift, shrink and expand.

MutableMotifDiscovererToolbox.InitMethodForDiffSM
This enum defines some constants for the method MutableMotifDiscovererToolbox.getSortedInitialParameters(DifferentiableSequenceScore[], InitMethodForDiffSM[], DiffSSBasedOptimizableFunction, int, OutputStream, int).

SignificantMotifOccurrencesFinder.JoinMethod
Interface for methods that combine several profiles over the same sequence into one common profile

SignificantMotifOccurrencesFinder.RandomSeqType

Classes in de.jstacs.motifDiscovery used by de.jstacs.sequenceScores.statisticalModels.differentiable

MotifDiscoverer
This is the interface that any tool for de-novo motif discovery should implement.

MotifDiscoverer.KindOfProfile
This enum can be used to determine which kind of profile should be returned.

Mutable
This interface allows to modify a motif model.

MutableMotifDiscoverer
This is the interface that any tool for de-novo motif discovery should implement that allows any modify-operations like shift, shrink and expand.

Classes in de.jstacs.motifDiscovery used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels

Mutable
This interface allows to modify a motif model.

Classes in de.jstacs.motifDiscovery used by de.jstacs.sequenceScores.statisticalModels.differentiable.mixture

MotifDiscoverer
This is the interface that any tool for de-novo motif discovery should implement.

MotifDiscoverer.KindOfProfile
This enum can be used to determine which kind of profile should be returned.

Mutable
This interface allows to modify a motif model.

MutableMotifDiscoverer
This is the interface that any tool for de-novo motif discovery should implement that allows any modify-operations like shift, shrink and expand.

Classes in de.jstacs.motifDiscovery used by de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif

MotifDiscoverer
This is the interface that any tool for de-novo motif discovery should implement.

MotifDiscoverer.KindOfProfile
This enum can be used to determine which kind of profile should be returned.

MutableMotifDiscoverer
This is the interface that any tool for de-novo motif discovery should implement that allows any modify-operations like shift, shrink and expand.

Classes in de.jstacs.motifDiscovery used by de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif

MotifDiscoverer
This is the interface that any tool for de-novo motif discovery should implement.

MotifDiscoverer.KindOfProfile
This enum can be used to determine which kind of profile should be returned.