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• PaGEJava() : broad.pda.geneexpression.PaGEJava
• Pair() : broad.core.datastructures.Pair< T1 > , jaligner.formats.Pair
• PairedEndReader() : umms.core.readers.PairedEndReader
• PairedEndReadIterator() : broad.pda.samtools.PairedEndReadIterator
• PairedEndWriter() : umms.core.writers.PairedEndWriter
• PairedReadAlignment() : umms.core.alignment.PairedReadAlignment
• pairedTStat() : broad.core.math.Statistics
• pairwiseNonoverlappingIgnoreStrand() : umms.core.utils.AnnotationUtils
• parse() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , broad.core.annotation.BasicAnnotationReader , broad.core.annotation.BasicGenomicAnnotationReader , broad.core.annotation.BEDGraphReader , broad.core.annotation.BEDReader , broad.core.annotation.GFFReader , broad.core.annotation.RepeatMaskerAnnotationReader , broad.core.annotation.ShortBEDReader , broad.core.parser.CommandLineParser , broad.core.parser.StringParser , broad.core.primer3.ComputeMIRScore , broad.core.sequence.FastaParser , broad.core.sequence.FastaQualityParser , broad.core.siphy.TreeScalerIO , broad.pda.datastructures.AlignmentsReader , broad.pda.geneexpression.agilent.AgilentToGCT , broad.pda.seq.fastq.FastqParser , jaligner.util.SequenceParser
• parseAgilentExperiment() : broad.pda.geneexpression.agilent.AgilentUtils
• parseAgilentExperimentGlobalStats() : broad.pda.geneexpression.agilent.AgilentUtils
• parseAndWrite() : broad.pda.tools.PSLXToSAM
• parseCDT() : broad.core.util.ParseGCTFile
• parseCHIPFile() : broad.core.util.GMTParser
• parseChipFile() : broad.core.util.ParseGCTFile
• parseCHIPFileByName() : broad.core.util.GMTParser
• parseCLS() : broad.core.util.ParseGCTFile
• parseCLSGroups() : broad.core.util.ParseGCTFile
• parseControlSamples() : broad.pda.geneexpression.agilent.AgilentUtils
• ParseException() : broad.core.error.ParseException
• parseExperimentInfoFile() : broad.pda.geneexpression.agilent.AgilentUtils
• parseExperimentInfoFileToGroup() : broad.pda.geneexpression.agilent.AgilentUtils
• parseExperimentInfoFileToGroups() : broad.pda.geneexpression.agilent.AgilentUtils
• parseExperimentInfoFileToName() : broad.pda.geneexpression.agilent.AgilentUtils
• parseExperimentInfoGroups() : broad.pda.geneexpression.agilent.AgilentUtils
• parseExperimentInfoNonControls() : broad.pda.geneexpression.agilent.AgilentUtils
• parseGeneList() : broad.core.util.ParseGCTFile
• ParseGeneSetFile() : broad.core.util.GMTParser
• ParseGMTFile() : broad.core.util.GMTParser
• parseGMXFile() : broad.core.util.GMTParser
• parseGoRawFiles() : broad.pda.gene.functionalAnnotation
• parseMaskFiles() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• parseNumericCls() : broad.core.util.ParseGCTFile
• parseRawPointRegions() : broad.core.annotation.BasicGenomicAnnotationReader
• parseRawRegions() : broad.core.annotation.BasicGenomicAnnotationReader
• passedQC() : broad.pda.geneexpression.ExpressionExperimentInfo
• passes() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.AlignmentDataModelStats , broad.pda.seq.segmentation.GenericAlignmentDataModel , broad.pda.seq.segmentation.ReadFilter< T >
• passesCutoff() : broad.pda.seq.segmentation.AlignmentDataModel , broad.pda.seq.segmentation.GenericAlignmentDataModel
• Path() : broad.pda.seq.graph.Path
• pathToGene() : umms.core.scripture.OrientedChromosomeTranscriptGraph
• pctOverlapWithRef() : broad.pda.annotation.Locus
• pearsonCorrelation() : broad.core.math.Statistics
• pearsonDistance() : broad.core.math.Statistics
• percentGC() : broad.core.primer3.PrimerUtils , broad.core.sequence.SequenceRegion
• percentGenomeOverlapping() : umms.core.annotation.Gene
• percentOverlapping() : umms.core.annotation.Gene
• PermutationDistribution() : broad.core.math.PermutationDistribution
• PermutationNotFoundException() : umms.core.coordinatesystem.PermutationNotFoundException
• permute() : broad.core.siphy.TreeScalerIO
• permuteAndAssignFDR() : broad.pda.differentialExpression.Permutations
• permuteAnnotation() : umms.core.coordinatesystem.CoordinateSpace , umms.core.coordinatesystem.GenomicSpace , umms.core.coordinatesystem.MaskedGenomicSpace , umms.core.coordinatesystem.TranscriptInGenomicSpace , umms.core.coordinatesystem.TranscriptomeSpace
• permuteAnnotationsOnChromosome() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• permuteColumns() : broad.core.motif.PositionWeightMatrix , broad.core.multiplealignment.MultipleAlignment
• permuteData() : broad.pda.differentialExpression.Permutations
• permuteDataByGroupSize() : broad.pda.differentialExpression.Permutations
• permuteRegions() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• PhastconsReader() : broad.core.siphy.PhastconsReader
• piEMIteration() : broad.core.siphy.EvolutionaryModel
• PiHMM() : broad.core.siphy.PiHMM
• Pileup() : broad.pda.seq.clip.Pileup
• placeInTree() : broad.core.datastructures.IntervalTree< V >
• plot() : broad.core.annotation.BasicGenomicAnnotationReader
• plus() : Jama.Matrix
• plusEquals() : Jama.Matrix
• poisson() : broad.core.math.ScanStatistics
• PoissonEnrichmentScore() : umms.core.model.score.PoissonEnrichmentScore
• PositionWeightColumn() : broad.core.motif.PositionWeightColumn
• PositionWeightMatrix() : broad.core.motif.PositionWeightMatrix
• PositionWeightMatrixIO() : broad.core.motif.PositionWeightMatrixIO
• PositionWeightMatrixModel() : broad.core.siphy.PositionWeightMatrixModel
• pow() : broad.core.datastructures.MatrixWithHeaders
• PrecomputeDataAlignmentStats() : broad.pda.seq.segmentation.PrecomputeDataAlignmentStats
• PreprocessDataSet() : broad.pda.geneexpression.PreprocessDataSet
• Primer3Exception() : broad.core.primer3.Primer3Exception
• print() : broad.core.motif.PositionWeightColumn , Jama.Matrix
• printHelpMessage() : broad.core.parser.CommandLineParser
• printKmer() : broad.core.motif.PositionWeightMatrix
• printProb() : broad.core.motif.PositionWeightColumn
• printRandModels() : broad.pda.gene.transcriptsNullModel
• printRandNeighborsInfo() : broad.pda.gene.NeighborsNullModel
• printRefinedWeightMatrix() : broad.core.motif.PositionWeightMatrix
• ProcessDataset() : broad.pda.geneexpression.agilent.analysis.ProcessDataset
• processOneAnnotationSet() : broad.pda.seq.rap.CollectAnnotationEnrichments
• processWindow() : umms.core.model.score.WindowProcessor< S extends WindowScore >
• pruneAndPeel() : broad.core.siphy.EvolutionaryModel
• pruneTree() : broad.core.siphy.ConservationUtils , broad.core.siphy.EvolutionaryModel
• PSLRecord() : umms.core.annotation.PSLRecord
• put() : broad.core.datastructures.IntervalTree< V >
• pvalue() : broad.core.math.Statistics