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

- f -

• F() : broad.core.math.ANOVA
• factorial() : broad.core.math.MathUtil
• FASTA() : jaligner.formats.FASTA
• FastaExtendPeaks() : broad.pda.seq.clip.FastaExtendPeaks
• FastaQualityIndex() : broad.core.sequence.FastaQualityIndex
• FastaSequenceIO() : broad.core.sequence.FastaSequenceIO
• FastqLibraryStats() : broad.pda.countreads.FastqLibraryStats
• FastqParser() : broad.pda.seq.fastq.FastqParser
• FastqSequence() : broad.pda.seq.fastq.FastqSequence
• FastqSplitterByBarcode() : broad.pda.seq.fastq.FastqSplitterByBarcode
• FDR() : broad.core.math.ComputeFDR , broad.core.math.Statistics
• FDRCorrect() : broad.core.math.Statistics
• FDRDistribution() : broad.core.math.FDRDistribution
• FDRExact() : broad.core.math.ComputeFDR
• FDRExactPrint() : broad.core.math.ComputeFDR
• FeatureSequenceAlignment() : umms.core.alignment.FeatureSequenceAlignment
• fileSize : broad.core.sequence.AbstractFastaParser
• filter() : broad.core.util.CollapseByIntersection
• FILTER_REJECT_DIR : broad.pda.seq.protection.MultiSampleScanPeakCaller
• filterByOverlap() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > , broad.pda.annotation.BEDFileParser
• filterByOverlapAndOrientation() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• filterByOverlapOfLastExon() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• filterByOverlapOfLastExonOrAfterLastExon() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• filterByScore() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• FilteredIterator() : umms.core.model.AlignmentModel.FilteredIterator , umms.core.model.JCSAlignmentModel.FilteredIterator
• FilterGCTFile() : broad.pda.geneexpression.FilterGCTFile
• filterGenesByExpression() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• filterInvariantGenes() : broad.core.datastructures.MatrixWithHeaders
• FilterMatrixByMinCutoff() : broad.pda.geneexpression.agilent.FilterMatrixByMinCutoff
• filterPaths() : broad.pda.seq.segmentation.ContinuousDataAlignmentModel
• filterValuesLargerThanUsingColumn() : broad.core.datastructures.MatrixWithHeaders
• filterValuesRangeUsingColumn() : broad.core.datastructures.MatrixWithHeaders
• filterValuesSmallerThanUsingColumn() : broad.core.datastructures.MatrixWithHeaders
• filterWindows() : broad.pda.seq.protection.TwoSampleScanSkellamPeakCaller
• find() : broad.core.annotation.BasicGenomicAnnotationReader , broad.core.datastructures.IntervalTree< V >
• findAllORFs() : umms.core.annotation.Gene
• findAllStartCodons() : umms.core.annotation.Gene
• findAnnotationFiles() : broad.pda.enrichment.EnrichmentUtils
• findByIndex() : broad.core.datastructures.IntervalTree< V >
• findClosest() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• findClosestForAll() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• findClosestNonOverlapping() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• findClosestNonoverlappingForAll() : broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >
• findCompatibleGenes() : broad.pda.gene.GeneWithIsoforms
• FindDiffrentialEnrichedRegions() : broad.pda.seq.chip.FindDiffrentialEnrichedRegions
• findEdge() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• FindEnrichedDepletedRegions() : broad.pda.rap.misc.FindEnrichedDepletedRegions
• findLongestORF() : umms.core.annotation.Gene
• FindProbesForGeneSet() : broad.pda.geneexpression.agilent.FindProbesForGeneSet
• findReachableTargetVertices() : broad.pda.seq.graph.ChromosomeWithBubblesJGraphT
• findUngappedSequenceChunks() : broad.core.sequence.Sequence
• finish() : broad.pda.seq.rap.rna.CollectRnaSeqMetrics
• finishedRegion() : umms.core.model.score.WindowProcessor< S extends WindowScore >.AbstractProcessor< S extends WindowScore > , umms.core.model.score.WindowProcessor< S extends WindowScore >
• firstField() : broad.core.parser.StringParser
• firstReadTranscriptionStrand() : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData
• FisherCombinedProbabilityTest() : broad.core.math.FisherCombinedProbabilityTest
• fitOmega() : broad.core.siphy.EvolutionaryModel , broad.core.siphy.tools.conservation.EstimateOmegaPerExon
• fitPI() : broad.core.siphy.EvolutionaryModel , broad.core.siphy.TreeScaler
• flatWeight() : broad.core.motif.PositionWeightColumn
• flatWeightMatrix() : broad.core.motif.PositionWeightMatrix
• floor() : broad.core.datastructures.MatrixWithHeaders
• FokI : broad.core.primer3.RestrictionEnzyme
• fold() : broad.core.math.Statistics
• FoldSignificance() : broad.pda.differentialExpression.FoldSignificance
• format() : jaligner.formats.CLUSTAL , jaligner.formats.FASTA , jaligner.formats.Format , jaligner.formats.Pair
• Fp() : broad.core.math.ScanStatistics
• FpWithBreaking() : broad.core.math.ScanStatistics
• FragmentAlignment() : umms.core.alignment.FragmentAlignment
• fromFullInfoString() : umms.core.annotation.BasicAnnotation
• fromString() : umms.core.annotation.Annotation.Strand
• FullyContainedFilter() : umms.core.annotation.filter.FullyContainedFilter
• fullyContainedReads : broad.pda.seq.clip.SampleData , broad.pda.seq.protection.SampleData , broad.pda.seq.protection.WindowScores
• fullyContains() : broad.core.sequence.SequenceRegion , umms.core.annotation.AbstractAnnotation , umms.core.annotation.Annotation
• functionalAnnotation() : broad.pda.gene.functionalAnnotation
• FwdIterator() : broad.core.datastructures.IntervalTree< V >.FwdIterator
• FWERDistribution() : broad.pda.differentialExpression.FWERDistribution