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## 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 `DifferentiableStatisticalModel`s, which can compute the gradient with respect to their parameters for a given input `Sequence`.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels | Provides `DifferentiableStatisticalModel`s that are directed graphical models.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture | Provides `DifferentiableSequenceScore`s that are mixtures of other `DifferentiableSequenceScore`s.
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.

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