- m -

• MAD() : broad.core.math.Statistics
• MAFAlignment() : broad.core.multiplealignment.MAFAlignment
• MAFIO() : broad.core.multiplealignment.MAFIO
• main() : broad.core.annotation.AnnotationUtils , broad.core.annotation.MaximumContiguousSubsequence , broad.core.datastructures.MatrixWithHeaderUtils , broad.core.math.ANOVA , broad.core.math.CombinationGenerator , broad.core.math.EmpiricalDistribution , broad.core.math.FDRDistribution , broad.core.math.Loess , broad.core.math.PermutationDistribution , broad.core.math.Statistics , broad.core.motif.misc.ComputeConservedMotifs , broad.core.motif.misc.ScoreMotifInstances , broad.core.motif.PositionWeightMatrixIO , broad.core.motif.PWMUtils , broad.core.motif.SequenceMotif , broad.core.motif.SequenceMotifCluster , broad.core.multiplealignment.AlignmentExtractor , broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignmentFactory , broad.core.overlaputils.GeneSetIntersect , broad.core.primer3.ComputeMIRScore , broad.core.primer3.isPCRLike , broad.core.primer3.PrimerUtils , broad.core.sequence.Extractor , broad.core.sequence.FastaQualityIndex , broad.core.sequence.FastaSequenceIO , broad.core.sequence.TranscribedRegions , broad.core.sequence.TranscribedSequenceComposition , broad.core.siphy.PiHMM , broad.core.siphy.tools.conservation.AverageBranchLength , broad.core.siphy.tools.conservation.BatchSubmitEstimateExon , broad.core.siphy.tools.conservation.ComputeKmersForRegion , broad.core.siphy.tools.conservation.ComputeMaxPercentileOfElements , broad.core.siphy.tools.conservation.ComputePercentageOfKmers , broad.core.siphy.tools.conservation.EstimateOmegaPerExon , broad.core.siphy.tools.conservation.SplitFile , broad.core.siphy.TreeScaler , broad.pda.annotation.BEDFileParser , broad.pda.countreads.AnnotationCounts , broad.pda.countreads.FastqLibraryStats , broad.pda.differentialExpression.BatchNorm , broad.pda.differentialExpression.CisVsTrans , broad.pda.differentialExpression.CollapseProjections , broad.pda.differentialExpression.ConvertToDiscreteMatrix , broad.pda.differentialExpression.FixedControlDifferentialExpression , broad.pda.differentialExpression.FoldSignificance , broad.pda.differentialExpression.GrabProbes , broad.pda.differentialExpression.GSAProjection , broad.pda.differentialExpression.MakePositionalGeneSets , broad.pda.differentialExpression.MergeGSEAOutputIntoMatrix , broad.pda.differentialExpression.RunAllGSEABatch , broad.pda.differentialExpression.RunDifferentialExpression , broad.pda.differentialExpression.RunGSEA , broad.pda.differentialExpression.RunTimeSeries , broad.pda.differentialExpression.SplitByName , broad.pda.gene.functionalAnnotation , broad.pda.gene.GeneTools , broad.pda.gene.NeighborAnalysis , broad.pda.geneexpression.agilent.AgilentToGCT , broad.pda.geneexpression.agilent.analysis.ProcessDataset , broad.pda.geneexpression.agilent.ClassifyAgilentLincProbes , broad.pda.geneexpression.agilent.CollapseProbesByMinPValue , broad.pda.geneexpression.agilent.CorrelationAgilentNanostring , broad.pda.geneexpression.agilent.CorrelationBetweenReplicates , broad.pda.geneexpression.agilent.ExtractSamplesAndLabel , broad.pda.geneexpression.agilent.FilterMatrixByMinCutoff , broad.pda.geneexpression.agilent.FindProbesForGeneSet , broad.pda.geneexpression.agilent.MakeCLSFiles , broad.pda.geneexpression.agilent.MakeCLSFromDescription , broad.pda.geneexpression.agilent.QCAgilentResults , broad.pda.geneexpression.clustering.ComputeCorrelationOfReplicates , broad.pda.geneexpression.clustering.HierarchicalClustering , broad.pda.geneexpression.clustering.RankOrder , broad.pda.geneexpression.ComputeHypergeomtricEnrichment , broad.pda.geneexpression.CountNums , broad.pda.geneexpression.FilterGCTFile , broad.pda.geneexpression.geneExpUtils , broad.pda.geneexpression.GlobalStats , broad.pda.geneexpression.GrabSpecificColumns , broad.pda.geneexpression.PaGEJava , broad.pda.geneexpression.PreprocessDataSet , broad.pda.rap.misc.FindEnrichedDepletedRegions , broad.pda.rnai.ExtractSequence , broad.pda.samtools.FilterFastqReads , broad.pda.samtools.FilterPairedReadsByMAQ , broad.pda.samtools.PairedEndTDF , broad.pda.samtools.SAMFragmentWriter , broad.pda.samtools.TrimFastqReads , broad.pda.seq.alignment.AlignmentUtils , broad.pda.seq.chip.ComputeEnrichments , broad.pda.seq.chip.FindDiffrentialEnrichedRegions , broad.pda.seq.chip.PeakFilter , broad.pda.seq.clip.FastaExtendPeaks , broad.pda.seq.clip.Pileup , broad.pda.seq.fastq.FastqSplitterByBarcode , broad.pda.seq.fastq.SplitAndTrimIndex , broad.pda.seq.fastq.SplitFastqByIndex , broad.pda.seq.protection.BatchedMultiSampleScanPeakCaller , broad.pda.seq.protection.MultiSampleScanPeakCaller , broad.pda.seq.protection.ReadSimulator , broad.pda.seq.protection.ReadSimulator2 , 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.RAPPeakCaller , broad.pda.seq.rap.RatioPermutationPeakCaller , broad.pda.seq.rap.rna.CollectRnaSeqMetrics , 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 , broad.pda.seq.segmentation.ContinuousDataAlignmentModel , broad.pda.seq.segmentation.GlobalSpliceFilter , broad.pda.seq.segmentation.PrecomputeDataAlignmentStats , broad.pda.seq.segmentation.utils.ReconstructionComparer , broad.pda.tools.PSLXToSAM , broad.projection.gsa.DefineGeneSignatures , broad.projection.gsa.ExtractGenes , broad.projection.gsa.GSAScoring , broad.projection.gsa.GsaUtils , umms.core.alignment.FeatureSequenceAlignment , umms.core.alignment.SmatchLike , umms.core.annotation.BasicAnnotation , umms.core.model.JCSAlignmentModel , umms.core.readers.PairedEndReader , umms.core.scripture.BuildScriptureCoordinateSpace , umms.core.scripture.statistics.ConnectDisconnectedTranscripts , umms.esat.CollapsedGeneLengths , umms.esat.ESAT , umms.esat.ESATDistanceCalculator
• makeBinnedIntervalModel() : broad.pda.gene.NeighborsNullModel
• MakeCLSFiles() : broad.pda.geneexpression.agilent.MakeCLSFiles
• MakeCLSFromDescription() : broad.pda.geneexpression.agilent.MakeCLSFromDescription
• makeDartThrowingModel() : broad.pda.gene.NeighborsNullModel
• makeDataMatrix() : broad.pda.geneexpression.agilent.AgilentUtils
• makeGenes() : broad.pda.annotation.BEDFileParser
• makeIntervalTree() : broad.core.util.CollapseByIntersection
• makeIntervalTreeFor3Prime() : broad.pda.annotation.BEDFileParser
• makeIntervalTreeForGeneExons() : broad.core.util.CollapseByIntersection
• makeIntervalTreeForGenes() : broad.core.util.CollapseByIntersection
• makeNaiveRandModel() : broad.pda.gene.NeighborsNullModel
• makePairs() : umms.core.alignment.AlignmentPair
• MakePositionalGeneSets() : broad.pda.differentialExpression.MakePositionalGeneSets
• makeRandTranscriptList() : broad.pda.gene.transcriptsNullModel
• manhattanDistance() : broad.core.math.Statistics
• MannWhitney() : broad.core.math.MannWhitney
• MannWhitneyPermutations() : broad.core.math.MannWhitneyPermutations
• mapChildToLargestParent() : umms.core.utils.AnnotationUtils
• mapChildToParents() : umms.core.utils.AnnotationUtils
• mapGenesToOverlappers() : broad.core.overlaputils.GeneSetIntersect
• mapParentsToChildren() : umms.core.utils.AnnotationUtils
• MappingQualityFilter() : umms.core.readFilters.MappingQualityFilter
• mapSamRecord() : broad.pda.seq.protection.ReadSimulator , broad.pda.seq.protection.ReadSimulator2
• MarkovModel() : broad.core.hmm.MarkovModel< T >
• mask() : broad.core.sequence.Sequence
• MaskedGenomicSpace() : umms.core.coordinatesystem.MaskedGenomicSpace
• maskSoftmaskedRegions() : broad.core.sequence.Sequence
• match() : broad.core.motif.PositionWeightMatrix , broad.core.motif.SequenceMotif , broad.core.motif.SequenceMotifCluster
• matchStartOnFirstSequence() : umms.core.alignment.SmithWatermanAlignment
• Matrix() : jaligner.matrix.Matrix , Jama.Matrix
• MatrixLoaderException() : jaligner.matrix.MatrixLoaderException
• MatrixWithHeaders() : broad.core.datastructures.MatrixWithHeaders
• max() : broad.core.datastructures.IntervalTree< V > , broad.core.math.MathUtil , broad.core.math.Statistics
• maxInt() : broad.core.math.Statistics
• maxMAD() : broad.core.math.Statistics
• maxmean() : broad.core.math.Statistics
• maxSelfComplementarity() : broad.core.primer3.HairpinKmer
• maxStdev() : broad.core.math.Statistics
• maxSubSum3() : broad.core.annotation.MaximumContiguousSubsequence
• mayHaveBlocks() : broad.core.annotation.BasicGenomicAnnotation , broad.core.annotation.BED , broad.core.annotation.GenomicAnnotation , broad.core.sequence.SequenceRegion
• mean() : broad.core.math.Statistics
• meanNormalizeColumns() : broad.core.datastructures.MatrixWithHeaders
• meanNormalizeRows() : broad.core.datastructures.MatrixWithHeaders
• measure() : broad.pda.geneexpression.clustering.AbsolutePearsonFunction , broad.pda.geneexpression.clustering.ClusterDistanceFunction , broad.pda.geneexpression.clustering.EuclideanDistance , broad.pda.geneexpression.clustering.PearsonDistance
• median() : broad.core.math.Statistics , broad.pda.differentialExpression.BatchNorm
• medianCenterColumns() : broad.core.datastructures.MatrixWithHeaders
• medianCenterColumnsThis() : broad.core.datastructures.MatrixWithHeaders
• medianCenterRows() : broad.core.datastructures.MatrixWithHeaders
• medianCenterRowsThis() : broad.core.datastructures.MatrixWithHeaders
• medianCollection() : broad.core.math.Statistics
• medianNormalizeColumns() : broad.core.datastructures.MatrixWithHeaders
• medianNormalizeRows() : broad.core.datastructures.MatrixWithHeaders
• MemeMotif() : broad.core.motif.meme.MemeMotif
• MemeResultReader() : broad.core.motif.meme.MemeResultReader
• memoryStats() : umms.core.scripture.BuildScriptureCoordinateSpace
• merge() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , broad.pda.annotation.BEDFileParser , broad.pda.datastructures.Alignments , broad.pda.gene.GeneTools
• mergeAllOverlappers() : broad.core.annotation.BasicLightweightAnnotation
• mergeByGtfGeneId() : broad.pda.annotation.BEDFileParser , broad.pda.gene.GeneTools
• MergeGSEAOutputIntoMatrix() : broad.pda.differentialExpression.MergeGSEAOutputIntoMatrix
• mergeOverlappingBlocks() : umms.core.utils.AnnotationUtils
• mergeOverlappingBlocksSingleOrientation() : umms.core.utils.AnnotationUtils
• mergePeaks() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• mergeRecords() : broad.core.sequence.FastaSequenceIO
• mergeSets() : broad.pda.gene.GeneTools
• metaAvg() : broad.core.math.Statistics
• min() : broad.core.datastructures.IntervalTree< V > , broad.core.math.Statistics
• minInt() : broad.core.math.Statistics
• minOverlapper() : broad.core.datastructures.IntervalTree< V >
• minus() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , broad.core.datastructures.MatrixWithHeaders , broad.core.sequence.SequenceRegion , broad.pda.annotation.BEDFileParser , Jama.Matrix , umms.core.annotation.Annotation , umms.core.annotation.AnnotationList< T extends Annotation > , umms.core.annotation.BasicAnnotation , umms.core.annotation.CompoundInterval
• minusEquals() : Jama.Matrix
• moveAnnotation() : umms.core.coordinatesystem.TranscriptomeSpace
• moveToCoordinate() : broad.core.sequence.SequenceRegion , umms.core.alignment.AbstractPairedEndAlignment , umms.core.annotation.Annotation , umms.core.annotation.BasicAnnotation , umms.core.annotation.CompoundInterval
• MultipleAlignment() : broad.core.multiplealignment.MultipleAlignment
• multiplyColumnsWithConstants() : broad.core.datastructures.MatrixWithHeaders
• MultiSampleScanPeakCaller() : broad.pda.seq.protection.MultiSampleScanPeakCaller
• MultiScore() : umms.core.model.score.MultiScore