- e -

• eig() : Jama.Matrix
• EigenvalueDecomposition() : Jama.EigenvalueDecomposition
• emitObservation() : broad.core.hmm.MarkovState< T >
• emitPath() : broad.core.hmm.MarkovModel< T >
• EmpiricalDistribution() : broad.core.math.EmpiricalDistribution
• encode() : broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment
• encodeAsMatrix() : broad.core.multiplealignment.MAFAlignment , broad.core.multiplealignment.MultipleAlignment , broad.core.siphy.TreeScaler
• encodeSequence() : broad.core.sequence.Sequence
• encodeSequenceAsVector() : broad.core.sequence.Sequence
• encodeSequenceIgnoreCase() : broad.core.sequence.Sequence
• EndInWindowCountScore() : umms.core.model.score.EndInWindowCountScore
• EnrichmentMetric() : broad.pda.enrichment.EnrichmentMetric
• ensureNoEmptyBins() : broad.core.math.EmpiricalDistribution
• entropy() : broad.core.math.Statistics
• enumerateAllKMers() : broad.core.primer3.ComputeOriginalScore
• eof() : broad.core.annotation.AnnotationHandler , broad.core.sequence.FastaHandler , broad.pda.datastructures.LocationAwareMatrix
• equalizeTranscriptEnds() : broad.pda.annotation.BEDFileParser
• equals() : broad.core.datastructures.Pair< T1 > , broad.core.motif.SequenceMotif , broad.core.sequence.SequenceRegion , broad.pda.seq.graph.Path , umms.core.alignment.FeatureSequenceAlignment.UnorderedGenePair , umms.core.alignment.FragmentAlignment , umms.core.alignment.PairedReadAlignment , umms.core.alignment.SingleEndAlignment , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation , umms.core.annotation.CompoundInterval , umms.core.annotation.SingleInterval , umms.core.feature.GeneWindow , umms.core.model.score.BasicScanStatisticScore , umms.core.model.score.CountScore , umms.core.model.score.ScanStatisticScore , umms.core.readFilters.SplicedReadFilter
• ESAT() : umms.esat.ESAT
• ESATDistanceCalculator() : umms.esat.ESATDistanceCalculator
• EstimateOmegaPerExon() : broad.core.siphy.tools.conservation.EstimateOmegaPerExon
• euclideanDistance() : broad.core.math.Statistics
• evaluate() : nextgen.core.readFilters.GenomicSpanFilter , nextgen.core.readFilters.PairedAndProperFilter , nextgen.core.readFilters.ReadsToReconstructFilter , umms.core.annotation.filter.FullyContainedFilter , umms.core.annotation.filter.OverlapFilter , umms.core.readFilters.MappingQualityFilter , umms.core.readFilters.PairedEndFilter , umms.core.readFilters.PCRDuplicateFilter , umms.core.readFilters.ReadEndsInFilter , umms.core.readFilters.ReadStartsInFilter , umms.core.readFilters.SameOrientationFilter , umms.core.readFilters.SplicedReadFilter , umms.core.readFilters.UniqueMappedReadsFilter
• EvolutionaryModel() : broad.core.siphy.EvolutionaryModel
• EvolutionaryModelParameters() : broad.core.siphy.EvolutionaryModelParameters
• evolve() : broad.core.siphy.EvolutionaryModel
• excludeByRowNames() : broad.core.datastructures.MatrixWithHeaders
• expand() : broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation
• expandUtrs() : broad.pda.gene.GeneWithIsoforms , umms.core.annotation.Gene
• expanedUtrs() : broad.pda.annotation.BEDFileParser
• ExpressionExperimentInfo() : broad.pda.geneexpression.ExpressionExperimentInfo
• extendAnnotation() : umms.core.annotation.Gene
• extendPairedEndReads() : broad.pda.samtools.PairedEndTDF
• extendSuperArgsForSampleAndChr() : broad.pda.seq.protection.BatchedMultiSampleScanPeakCaller
• extractBarcodeFromFastq() : broad.pda.seq.fastq.SplitFastqByIndex
• extractGFFRegions() : broad.core.multiplealignment.AlignmentExtractor
• Extractor() : broad.core.sequence.Extractor
• extractRecords() : broad.core.sequence.FastaSequenceIO
• extractRecordsIntoSequenceList() : broad.core.sequence.FastaSequenceIO
• extractRecordsWithIDLike() : broad.core.sequence.FastaSequenceIO
• extractRecordsWithIDsMatching() : broad.core.sequence.FastaSequenceIO
• extractRegion() : broad.core.sequence.FastaSequenceIO , broad.pda.feature.genome.Chromosome
• extractRegionBasedOnGC() : broad.core.sequence.Sequence , broad.core.sequence.SequenceRegion
• extractRegions() : broad.core.sequence.FastaSequenceIO , broad.pda.feature.genome.Chromosome
• ExtractSamplesAndLabel() : broad.pda.geneexpression.agilent.ExtractSamplesAndLabel