See: Description
Interface | Description |
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AffinityEvaluatorDriver.EvaluatorFunction | |
CREModel |
Interface for defining different ways of modeling cis-regulatory elements.
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ProbCREModel |
Interface that extends CREModel to include methods specific to probabilistic models.
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Class | Description |
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AffinityEvaluator |
Methods to evaluate a CREModel on affinity data.
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AffinityEvaluatorDriver |
A driver for the AffinityEvaluator class.
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AffinityEvaluatorDriver.AffinityFileFilter |
A file filter that accepts only affinity files.
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AffinityEvaluatorDriver.BackgroundEvalFunc |
Just a special designation that this requires a background.
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AffinityEvaluatorDriver.FPFNEvalFunc | |
AffinityEvaluatorDriver.ROCEvalFunc |
Only allows ProbCREModel's to be scored.
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AffinityEvaluatorDriver.SiteFileFilter |
A file filter that accepts only site files and affinity files.
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AffinityEvaluatorDriver.TestModel | |
ConsensusSequence |
Implementation of the consensus sequence model that keeps track of reverse complement status.
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KMismatchModel |
Implementation of the k-mismatch model that keeps track of reverse complement status.
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KRModel |
An implementation of the non-parametric model described by King and Roth.
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ModelEvaluator |
Command-line program for evaluating different CRE models.
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PLConsensusModel |
Variation on the ConsensusSequence that defines the consensus based on a notion of minimum distance from the median.
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PWM |
Implementation of the position-weight matrix model as a 2D array of the counts for each base at each position; keeps track of reverse
complement status.
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PWMEvaluator |
Command-line program for evaluating a PWM at different stringencies.
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Exception | Description |
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ExpansionTooLargeException |
An exception for specifying the a pwm, kmm, or consensus expands to too many bases to be computable.
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