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

- d -

• data : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData
• dataInverse() : broad.core.datastructures.MatrixWithHeaders
• decode() : broad.core.sequence.Sequence
• decodeShort() : broad.core.multiplealignment.MultipleAlignment
• DecollapseByIntronLocation() : broad.core.util.CollapseByIntersection
• DecollapseByIntronLocationOld() : broad.core.util.CollapseByIntersection
• DecollapseByIntronLocationWorking() : broad.core.util.CollapseByIntersection
• dedup() : broad.pda.annotation.BEDFileParser , broad.pda.gene.GeneWithIsoforms
• DEFAULT_ALPHABET_SIZE : broad.core.motif.PositionWeightColumn
• DEFAULT_GAP_EXTEND_PENALTY : umms.core.alignment.FeatureSequenceAlignment , umms.core.alignment.SmithWatermanAlignment
• DEFAULT_GAP_OPEN_PENALTY : umms.core.alignment.FeatureSequenceAlignment , umms.core.alignment.SmithWatermanAlignment
• DEFAULT_INS_SIZE_PVAL : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• DEFAULT_INSERT_SIZE_FUDGE : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• DEFAULT_MAKE_GENE_OVERLAP : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• DEFAULT_MATCH_SCORE : umms.core.alignment.FeatureSequenceAlignment , umms.core.alignment.SmithWatermanAlignment
• DEFAULT_MIN_MAPPING_QUALITY : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• DEFAULT_MISMATCH_SCORE : umms.core.alignment.FeatureSequenceAlignment , umms.core.alignment.SmithWatermanAlignment
• DEFAULT_REGION_TOTAL : umms.core.model.score.CountScore , umms.core.model.score.PoissonEnrichmentScore
• DEFAULT_VALUE : umms.core.model.score.AbstractListScore
• DefineGeneSignatures() : broad.projection.gsa.DefineGeneSignatures
• degenerateCodonStarts : broad.core.multiplealignment.AlignmentExtractor
• delete() : broad.pda.feature.genome.Chromosome , broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• DEPLETED : broad.pda.seq.rap.RatioPermutationPeakCaller , broad.pda.seq.rap.SkellamKLPeakCaller
• destroyFileHandle() : broad.core.multiplealignment.MAFIO
• det() : Jama.LUDecomposition , Jama.Matrix
• DIAGONAL : jaligner.Directions
• diff() : broad.core.math.Statistics
• differenceByGenomicRegion() : broad.pda.annotation.BEDFileParser
• DifferentialExpression() : broad.pda.differentialExpression.DifferentialExpression
• digest() : broad.core.primer3.RestrictionEnzyme
• DirectoryInstalledGenomeAssembly() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• DISCRETE_EXTENSION : broad.pda.seq.rap.CollectAnnotationEnrichments
• disect() : broad.core.annotation.BasicGenomicAnnotation , broad.core.sequence.SequenceRegion , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation
• dispose() : broad.core.datastructures.JCSCache
• distance() : broad.pda.geneexpression.clustering.Kmeans
• distanceBetween() : broad.pda.datastructures.Alignments
• distanceFrom() : broad.core.motif.PositionWeightMatrix
• distanceToNearestNonOverlapper() : umms.core.annotation.Gene
• distanceToOppositeStrand5primeNeighbor() : broad.pda.annotation.Locus
• doesOverlap() : broad.core.datastructures.IntervalTree< V >
• doRepeatListNeedsCleanup() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• doWork() : broad.pda.samtools.FilterFastqReads , broad.pda.samtools.FilterPairedReadsByMAQ , broad.pda.samtools.PairedEndTDF , broad.pda.samtools.TrimFastqReads , broad.pda.seq.rap.BuildRatioNullDistribution , broad.pda.seq.rap.CalculateCoverageStats , broad.pda.seq.rap.CollectAnnotationEnrichments , broad.pda.seq.rap.CountProbes , broad.pda.seq.rap.CountReads , broad.pda.seq.rap.DistanceToBED , broad.pda.seq.rap.GCContent , broad.pda.seq.rap.PlotAggregateRegions , broad.pda.seq.rap.RatioPermutationPeakCaller , broad.pda.seq.rap.rna.CountReads , broad.pda.seq.rap.ShuffleBAM , broad.pda.seq.rap.ShuffleBED , broad.pda.seq.rap.SkellamKLPeakCaller , broad.pda.seq.rap.SlideAndCalculate , broad.pda.seq.rap.SlideAndCount , broad.pda.seq.rap.UnmarkDuplicates , umms.core.scripture.statistics.ConnectDisconnectedTranscripts
• drawAutosome() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• drawChromosome() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• drawInitialState() : broad.core.hmm.MarkovModel< T >
• drawNextState() : broad.core.hmm.MarkovModel< T >
• drawRandomAutosomeRegion() : broad.pda.feature.genome.DirectoryInstalledGenomeAssembly
• drawRandomRegion() : broad.pda.feature.genome.Chromosome , broad.pda.feature.genome.DirectoryInstalledGenomeAssembly