Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

[detail level 123456]

▼Nbroad
▼Ncore
►Nannotation
CAnnotationFactory< T extends LightweightGenomicAnnotation >
CAnnotationFactoryFactory
CAnnotationHandler
CAnnotationReader< T extends GenomicAnnotation >
CAnnotationReaderFactory
CAnnotationUtils
CBasicAnnotationReader
CBasicGenomicAnnotation
CBasicGenomicAnnotationReader
CBasicLightweightAnnotation
CBasicTwoSubjectAnnotation
CBED
CBEDGraph
CBEDGraphReader
CBEDReader
CFeature
CGenomicAnnotation
CGenomicAnnotationFilter< T extends LightweightGenomicAnnotation >
CGFF
CGFFReader
CLightweightGenomicAnnotation
CMaximumContiguousSubsequence
CRepeatMaskerAnnotation
CRepeatMaskerAnnotationReader
CShortBED
CShortBEDReader
CTwoSubjectAnnotation
►Ndatastructures
CGenericRootedTree< T >
CIllegalTreeOperationException
CInterval
►CIntervalTree< V >
CFwdIterator
COverlapIterator
CRevIterator
►CJCSCache
CJCSNodeIterator
CMatrixWithHeaders
CMatrixWithHeaderUtils
CPair< T1 >
CReversibleIterator< E >
►Nerror
CParseException
►Nhmm
CBadModelException
CMarkovModel< T >
CMarkovState< T >
►Nmath
CANOVA
CCombinationGenerator
CComputeFDR
CDistribution
CEmpiricalDistribution
CFDRDistribution
CFisherCombinedProbabilityTest
CKSTest
CLoess
CMannWhitney
CMannWhitneyPermutations
CMathUtil
CPermutationDistribution
CScanStatistics
CStatistics
CUnfairDie
CWilcox2Sample
►Nmotif
►Nmeme
CAMEResultReader
CMemeMotif
CMemeResultReader
►Nmisc
CComputeConservedMotifs
CScoreMotifInstances
CPositionWeightColumn
CPositionWeightMatrix
CPositionWeightMatrixIO
CPWMUtils
CSearchException
CSequenceMotif
CSequenceMotifCluster
►Nmultiplealignment
CAlignmentExtractor
CFastaMultipleAlignmentIO
CMAFAlignment
CMAFIO
CMultipleAlignment
CMultipleAlignmentFactory
CMultipleAlignmentIO
CMultipleAlignmentIOFactory
CPhylipInterleavedMultipleAlignmentIO
CPhylipSequencialMultipleAlignmentIO
►Noverlaputils
CGeneSetIntersect
►Nparser
CCommandLineParser
CStringParser
►Nprimer3
CComputeMIRScore
CComputeOriginalScore
CCrossJunctionPCRDesigner
CHairpinKmer
CisPCRLike
CPrimer3Exception
CPrimer3PickingSummary
CPrimer3PrimerPickingResult
CPrimerUtils
CRestrictionEnzyme
►Nsequence
CAbstractFastaParser
CExtractor
CFastaHandler
CFastaParser
CFastaQualityBinaryIO
CFastaQualityHandler
CFastaQualityIndex
CFastaQualityParser
CFastaSequenceIO
CSequence
CSequenceRegion
CSequenceRegionWindow
CSequenceUtils
CTranscribedRegions
CTranscribedSequenceComposition
CWindowSlider
►Nsiphy
►Ntools
►Nconservation
CAverageBranchLength
CBatchSubmitEstimateExon
CComputeKmersForRegion
CComputeMaxPercentileOfElements
CComputePercentageOfKmers
CEstimateOmegaPerExon
CSplitFile
CConservationUtils
CConservedPWMScanner
CEvolutionaryModel
CEvolutionaryModelParameters
CFit
CPhastconsReader
CPiHMM
CPositionWeightMatrixModel
CScaledWindowParserListener
CStationaryDistributionIO
CTreeScaler
CTreeScalerIO
CUnableToFitException
►Nutil
CChromosomeStringComparator
CCLUtil
CCollapseByIntersection
CGMTParser
CParseGCTFile
▼Npda
►Nannotation
CBEDFileParser
CGTFFileParser
CLocus
►Ncountreads
CAnnotationCounts
CFastqLibraryStats
►Ndatastructures
CAlignments
CAlignmentsReader
CLocationAwareMatrix
►NdifferentialExpression
CBatchNorm
CCisVsTrans
CCollapseProjections
CConvertToDiscreteMatrix
CDifferentialExpression
CDifferentialScoring
CFixedControlDifferentialExpression
CFoldSignificance
CFWERDistribution
CGrabProbes
CGSAProjection
CMakePositionalGeneSets
CMergeGSEAOutputIntoMatrix
CPermutations
CRunAllGSEABatch
CRunDifferentialExpression
CRunGSEA
CRunTimeSeries
CSplitByName
►Nenrichment
CEnrichmentMetric
CEnrichmentUtils
►Nfeature
►Ngenome
CChromosome
CDirectoryInstalledGenomeAssembly
►Ngene
CfunctionalAnnotation
CGeneTools
CGeneWithIsoforms
CNeighborAnalysis
CNeighborsNullModel
CtranscriptsNullModel
►Ngeneexpression
►Nagilent
►Nanalysis
CProcessDataset
CAgilentArrayStats
CAgilentProbe
CAgilentToGCT
CAgilentUtils
CClassifyAgilentLincProbes
CCollapseProbesByMinPValue
CCorrelationAgilentNanostring
CCorrelationBetweenReplicates
CExtractSamplesAndLabel
CFilterMatrixByMinCutoff
CFindProbesForGeneSet
CMakeCLSFiles
CMakeCLSFromDescription
CQCAgilentResults
►Nclustering
CAbsolutePearsonFunction
CCluster
CClusterDistanceFunction
CComputeCorrelationOfReplicates
CCorrelationMatrix
CEuclideanDistance
CHierarchicalClustering
CKmeans
CPearsonDistance
CRankOrder
CComputeHypergeomtricEnrichment
CCountNums
CExpressionExperimentInfo
CFilterGCT
CFilterGCTFile
CgeneExpUtils
CGlobalStats
CGrabSpecificColumns
CPaGEJava
CPreprocessDataSet
CScoreDiffGenes
►Nrap
►Nmisc
CFindEnrichedDepletedRegions
►Nrnai
CExtractSequence
CRNAiGeneAnnotation
►Nsamtools
CFilterFastqReads
CFilterPairedReadsByMAQ
CPairedEndReadIterator
CPairedEndTDF
CSAMFragmentWriter
CSAMPairedEndFileReader
CTrimFastqReads
CWrappedIterator
►Nseq
►Nalignment
CAlignmentUtils
CStoredAlignmentStats
►Nchip
CComputeEnrichments
CFindDiffrentialEnrichedRegions
CPeakFilter
►Nclip
CFastaExtendPeaks
CGenomeSpaceSampleData
CPileup
CSampleData
►Nfastq
CFastqParser
CFastqSequence
CFastqSplitterByBarcode
CSplitAndTrimIndex
CSplitFastqByIndex
►Ngraph
►CChromosomeWithBubblesJGraphT
CEdgeSourceType
CPath
►Nprotection
CBatchedMultiSampleScanPeakCaller
CGenomeSpaceSampleData
CMultiSampleScanPeakCaller
CReadSimulator
CReadSimulator2
CSampleData
CTwoSampleScanSkellamPeakCaller
CWindowScores
►Nrap
►Nrna
CCollectRnaSeqMetrics
CCountReads
CTranscriptomeCommandLineProgram
CTranscriptomeScoringProgram
CBuildRatioNullDistribution
CCalculateCoverageStats
CCollectAnnotationEnrichments
CCountProbes
CCountReads
CDistanceToBED
CGCContent
CGenomeCommandLineProgram
CGenomeScoringProgram
CPlotAggregateRegions
CRAPPeakCaller
CRatioPermutationPeakCaller
CShuffleBAM
CShuffleBED
CSkellamKLPeakCaller
CSkellamScore
CSlideAndCalculate
CSlideAndCount
CUnmarkDuplicates
►Nsegmentation
►Nutils
CReconstructionComparer
CAlignmentDataModel
CAlignmentDataModelStats
CContinuousDataAlignmentModel
CDefineSourceAndSinkFromPairedEnds
CGeneCounts
CGenericAlignmentDataModel
CGeneScore
CGenomeWithGaps
CGenomeWithGaps2
CGlobalSpliceFilter
CPrecomputeDataAlignmentStats
CReadCountNormalizer
CReadFilter< T >
CWrappedIGVIterator
►Ntools
CPSLXToSAM
▼Nprojection
►Ngsa
CDefineGeneSignatures
CExtractGenes
CGeneSetEnrichment
CGSAScoring
CGsaUtils
▼Njaligner
▼Nformats
CCLUSTAL
CFASTA
CFormat
CFormatFactory
CPair
▼Nmatrix
CMatricesCompartor
CMatrix
CMatrixGenerator
CMatrixLoaderException
▼Nutil
CCommons
CSequenceParser
CSequenceParserException
CAlignment
CCell
CDirections
CMarkups
CNeedlemanWunsch
CNeedlemanWunschGotoh
CSequence
CSmithWatermanGotoh
CTracebackNode
▼NJama
▼Nutil
CMaths
CCholeskyDecomposition
CEigenvalueDecomposition
CLUDecomposition
CMatrix
CQRDecomposition
CSingularValueDecomposition
▼Nnextgen
▼Ncore
►NreadFilters
CGenomicSpanFilter
CPairedAndProperFilter
CReadsToReconstructFilter
▼Numms
▼Ncore
►Nalignment
CAbstractPairedEndAlignment
CAlignment
CAlignmentPair
CChromosomeInconsistencyException
►CFeatureSequenceAlignment
CUnorderedGenePair
CFragmentAlignment
CPairedEndAlignmentFactory
CPairedReadAlignment
►CSingleEndAlignment
CWrapSamRecord
CSmatchLike
CSmithWatermanAlignment
►Nannotation
►Nfilter
CFullyContainedFilter
COverlapFilter
CAbstractAnnotation
CAbstractAnnotationCollection< T extends Annotation >
►CAnnotation
CStrand
CAnnotationCollection< T extends Annotation >
CAnnotationFileReader
CAnnotationList< T extends Annotation >
CBasicAnnotation
CCompoundInterval
CGene
CPSLRecord
CSingleInterval
►Ncoordinatesystem
CAnnotationOutOfBoundsException
CCoordinateSpace
CGenomicSpace
CMaskedGenomicSpace
CPermutationNotFoundException
CShuffledIterator< T extends Annotation >
CTranscriptInGenomicSpace
►CTranscriptomeSpace
CGeneTree
►Nexception
CIncompleteMethodImplementationException
CRuntimeIOException
►Nfeature
CGeneWindow
CGenomeWindow
CWindow
►Ngeneral
CCloseableFilterIterator< T >
CPredicates
►CTabbedReader
CFactory< T >
►Nmodel
►Nscore
CAbstractListScore
CBasicScanStatisticScore
CBinomialEnrichmentScore
CCountScore
CCoverageScore
CEndInWindowCountScore
CLengthScore
CMultiScore
CNewRatioScore
CPoissonEnrichmentScore
CRatioScore
CScanStatisticScore
CStartInWindowCountScore
CSumScore
CWindowAllScore
►CWindowProcessor< S extends WindowScore >
CAbstractProcessor< S extends WindowScore >
►CWindowScore
CAbstractWindowScore
CWindowScoreIterator< T extends WindowScore >
►CAlignmentModel
CAlignmentCount
CFilteredIterator
CNodeIterator
CWrapAlignmentCountIterator
►CJCSAlignmentModel
CAlignmentCount
CFilteredIterator
CNodeIterator
CWrapAlignmentCountIterator
►Nreaders
CPairedEndReader
►NreadFilters
CMappingQualityFilter
CPairedEndFilter
CPCRDuplicateFilter
CReadEndsInFilter
CReadStartsInFilter
CSameOrientationFilter
CSplicedReadFilter
CUniqueMappedReadsFilter
►Nscripture
►Nstatistics
CConnectDisconnectedTranscripts
CBuildScriptureCoordinateSpace
COrientedChromosomeTranscriptGraph
►Nutils
CAnnotationUtils
►Nwriters
CPairedEndWriter
▼Nesat
CCollapsedGeneLengths
CESAT
CESATDistanceCalculator