Here is a list of all class members with links to the classes they belong to:

- r -

• random : broad.pda.seq.protection.MultiSampleScanPeakCaller , Jama.Matrix
• RANDOM_SEED : broad.pda.seq.rap.BuildRatioNullDistribution , broad.pda.seq.rap.ShuffleBAM
• randomPermutation() : broad.core.math.Statistics
• randomPermuteColumns() : broad.core.datastructures.MatrixWithHeaders
• rank() : broad.core.datastructures.MatrixWithHeaders , broad.core.math.MannWhitney , broad.core.math.Statistics , Jama.Matrix , Jama.SingularValueDecomposition
• rankOrder() : broad.core.math.MannWhitney
• RankOrder() : broad.pda.geneexpression.clustering.RankOrder
• RAPPeakCaller() : broad.pda.seq.rap.RAPPeakCaller
• RatioScore() : umms.core.model.score.RatioScore
• rawRegions() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• read() : Jama.Matrix , umms.core.annotation.AnnotationFileReader , umms.core.general.TabbedReader
• READ_LIST_FILE : broad.pda.samtools.FilterFastqReads
• readCigarFlag : umms.core.writers.PairedEndWriter
• readDstFile() : broad.core.math.Loess
• ReadEndsInFilter() : umms.core.readFilters.ReadEndsInFilter
• ReadSimulator2() : broad.pda.seq.protection.ReadSimulator2
• readSiphyOutToBed() : broad.pda.annotation.BEDFileParser
• readStartFlag : umms.core.writers.PairedEndWriter
• ReadStartsInFilter() : umms.core.readFilters.ReadStartsInFilter
• reconstructGeneEnds() : umms.esat.ESAT , umms.esat.ESATDistanceCalculator
• ReconstructionComparer() : broad.pda.seq.segmentation.utils.ReconstructionComparer
• reduceToDifference() : broad.core.annotation.BasicGenomicAnnotation
• REF : broad.pda.seq.rap.DistanceToBED
• REFERENCE_SEQUENCE : broad.pda.seq.rap.GCContent
• refreshAttributeMap() : umms.core.alignment.AbstractPairedEndAlignment
• refreshPvalue() : umms.core.model.score.BinomialEnrichmentScore , umms.core.model.score.CountScore
• refreshScanPvalue() : umms.core.model.score.ScanStatisticScore
• REG_PATTERN : broad.core.annotation.BasicGenomicAnnotationReader
• REGION : broad.pda.seq.rap.GenomeCommandLineProgram
• region : umms.core.coordinatesystem.ShuffledIterator< T extends Annotation >
• registerFormat() : jaligner.formats.FormatFactory
• remove() : broad.core.datastructures.IntervalTree< V >.FwdIterator , broad.core.datastructures.IntervalTree< V >.OverlapIterator , broad.core.datastructures.IntervalTree< V > , broad.core.datastructures.IntervalTree< V >.RevIterator , broad.core.datastructures.JCSCache.JCSNodeIterator , broad.core.datastructures.ReversibleIterator< E > , broad.core.multiplealignment.MultipleAlignment , broad.core.sequence.WindowSlider , broad.pda.annotation.BEDFileParser , broad.pda.samtools.PairedEndReadIterator , broad.pda.samtools.WrappedIterator , broad.pda.seq.fastq.FastqParser , broad.pda.seq.segmentation.WrappedIGVIterator , umms.core.coordinatesystem.ShuffledIterator< T extends Annotation > , umms.core.general.CloseableFilterIterator< T > , umms.core.model.AlignmentModel.FilteredIterator , umms.core.model.AlignmentModel.NodeIterator , umms.core.model.AlignmentModel.WrapAlignmentCountIterator , umms.core.model.JCSAlignmentModel.FilteredIterator , umms.core.model.JCSAlignmentModel.NodeIterator , umms.core.model.JCSAlignmentModel.WrapAlignmentCountIterator , umms.core.model.score.WindowScoreIterator< T extends WindowScore >
• REMOVE_MATE : broad.pda.samtools.FilterPairedReadsByMAQ
• removeAnnotation() : umms.core.annotation.AnnotationList< T extends Annotation >
• removeAtEnd : broad.pda.samtools.TrimFastqReads
• removeAtStart : broad.pda.samtools.TrimFastqReads
• removeAtSymbolFromName() : broad.pda.seq.fastq.FastqSequence
• removeEdge() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT , broad.pda.seq.graph.Path
• removeExtraScores() : broad.core.annotation.BasicLightweightAnnotation , broad.core.annotation.LightweightGenomicAnnotation , broad.core.sequence.SequenceRegion
• removeFilter() : umms.core.model.AlignmentModel , umms.core.model.JCSAlignmentModel
• removeInterval() : umms.core.annotation.CompoundInterval
• removeOverlappingRows() : broad.pda.datastructures.LocationAwareMatrix
• removeSingeleExon() : broad.pda.annotation.BEDFileParser
• removeSmallTranscripts() : broad.pda.annotation.BEDFileParser
• removeSpanningGapNodes() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• removeVertex() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• RepeatMaskerAnnotation() : broad.core.annotation.RepeatMaskerAnnotation
• repeatMaskerAnnotationFactory : broad.core.annotation.AnnotationFactoryFactory
• RepeatMaskerAnnotationReader() : broad.core.annotation.RepeatMaskerAnnotationReader
• replaceFileExtension() : broad.core.util.CLUtil
• reset() : broad.core.math.CombinationGenerator
• resetPI() : broad.core.siphy.EvolutionaryModel
• resetProbWithNullPriorProb() : broad.core.motif.PositionWeightColumn
• resetToUniformProb() : broad.core.motif.PositionWeightColumn
• resetTreeCache() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.ContinuousDataAlignmentModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• restartIterator() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• RestrictionEnzyme() : broad.core.primer3.RestrictionEnzyme
• reverse() : broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment , broad.core.primer3.ComputeMIRScore , broad.core.sequence.Sequence
• reverseComplement() : broad.core.motif.PositionWeightMatrix , broad.core.primer3.ComputeMIRScore , broad.pda.rnai.ExtractSequence
• reverseIterator() : broad.core.datastructures.IntervalTree< V >
• reverseSequence() : broad.core.sequence.Sequence
• ReversibleIterator() : broad.core.datastructures.ReversibleIterator< E >
• RevIterator() : broad.core.datastructures.IntervalTree< V >.RevIterator
• RIGHT_MARGIN : broad.core.annotation.BasicGenomicAnnotationReader
• rightIntersect() : broad.core.math.EmpiricalDistribution
• RNAiGeneAnnotation() : broad.pda.rnai.RNAiGeneAnnotation
• roll() : broad.core.math.UnfairDie
• roots() : broad.core.math.MathUtil
• round() : broad.core.datastructures.MatrixWithHeaders
• rowDensityNormalization() : broad.core.datastructures.MatrixWithHeaders
• rowDimension() : broad.core.datastructures.MatrixWithHeaders
• RPIDecomposition() : broad.core.siphy.EvolutionaryModel
• RPKM_OFFSET : umms.core.model.score.NewRatioScore , umms.core.model.score.RatioScore , umms.core.model.score.WindowAllScore
• RPKM_RATIO_OFFSET : broad.pda.seq.rap.SlideAndCalculate
• runBackwardAlgorithm() : broad.core.hmm.MarkovModel< T > , broad.core.siphy.PiHMM
• RunDifferentialExpression() : broad.pda.differentialExpression.RunDifferentialExpression
• runForwardAlgorithm() : broad.core.hmm.MarkovModel< T > , broad.core.siphy.PiHMM
• runForwardAlgorithmNoRescaling() : broad.core.hmm.MarkovModel< T >
• RunGSEA() : broad.pda.differentialExpression.RunGSEA
• runKmeans() : broad.pda.geneexpression.clustering.Kmeans
• RuntimeIOException() : umms.core.exception.RuntimeIOException
• RunTimeSeries() : broad.pda.differentialExpression.RunTimeSeries