Uses of Package
de.jstacs.motifDiscovery

Packages that use de.jstacs.motifDiscovery

Package	Description
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.localMixture
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

Class and Description
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

Class and Description
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

Class and Description
Mutable This interface allows to modify a motif model.

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

Class and Description
Mutable This interface allows to modify a motif model.

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

Class and Description
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

Class and Description
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

Class and Description
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.