All Classes

  • AcgtTree
  • AlleleCountStats
  • ArrayUtil
  • AutoHashMap
  • Average
  • AverageInt
  • BasesChangeCounter
  • BedAnnotationOutputFormatter
  • BedFileIterator
  • BedOutputFormatter
  • BigBedFileIterator
  • BinarySequence
  • Binomial
  • BinSeqFileIterator
  • BioType
  • BitUtil
  • BlackBoxEvent
  • BlastResultEntry
  • BlastResultFileIterator
  • BooleanMutable
  • CatalystActivity
  • Cds
  • Chromosome
  • ChromosomeSimpleName
  • ChrPosScoreList
  • ChrPosStats
  • CircularCorrection
  • CochranArmitageTest
  • Coder
  • CodonChange
  • CodonChangeDel
  • CodonChangeDup
  • CodonChangeIns
  • CodonChangeInterval
  • CodonChangeInv
  • CodonChangeMixed
  • CodonChangeMnp
  • CodonChangeSnp
  • CodonChangeStructural
  • CodonTable
  • CodonTables
  • CombinatorialIterator
  • CommandLine
  • CompareByValue
  • CompareByValue
  • CompareEffects
  • CompareToEnsembl
  • CompareToVep
  • Compartment
  • Complex
  • Config
  • CountByKey
  • CountByType
  • Counter
  • CounterDouble
  • CountFragments
  • CountReads
  • CountReadsOnMarkers
  • Coverage
  • CoverageByType
  • CoverageChr
  • CreateSpliceSiteTestCase
  • Custom
  • CvTerm
  • CytoBands
  • Depolymerisation
  • Diff
  • DistanceResult
  • DnaAndQualitySequence
  • DnaAndQualitySequenceWithId
  • DnaCoder
  • DnaNSequence
  • DnaQualityCoder
  • DnaQualSubsequenceComparator
  • DnaSeqFileIterator
  • DnaSeqIdFileIterator
  • DnaSeqPeFileIterator
  • DnaSequence
  • DnaSequenceByte
  • DnaSequenceId
  • DnaSequencePe
  • DnaSubsequenceComparator
  • Download
  • Downstream
  • EffectType
  • EffFormatVersion
  • Embl
  • EmblFile
  • EnrichmentAlgorithm
  • EnrichmentAlgorithm.EnrichmentAlgorithmType
  • EnrichmentAlgorithmGreedy
  • EnrichmentAlgorithmGreedyVariableSize
  • Entity
  • Entity.TransferFunction
  • ErrorWarningType
  • Event
  • ExecuteOsCommand
  • Exon
  • Exon.ExonSpliceType
  • ExonSpliceCharacterizer
  • FastaFileIterator
  • Fastq2Fastq
  • FastqFileIterator
  • FastqSplit
  • FastqTools
  • FastqTrimmer
  • FastqTrimmerAdrian
  • FastqTrimmerMedian
  • Feature
  • Feature.Type
  • FeatureCoordinates
  • Features
  • FeaturesFile
  • FileIndexChrPos
  • FileIterator
  • Filter
  • FindRareAaIntervals
  • FisherExactTest
  • FisherPValueAlgorithm
  • FisherPValueGreedyAlgorithm
  • FloatStats
  • FrameType
  • GenBank
  • GenBankFile
  • Gene
  • Gene.GeneType
  • GeneCountByTypeTable
  • GeneIds
  • GenericMarker
  • GenericMarkerFileIterator
  • Genes
  • GeneSet
  • GeneSets
  • GeneSetsRanked
  • GeneStats
  • Genome
  • GenomicSequences
  • Genotypes
  • GenotypeStats
  • GenotypeVector
  • Gff3FileIterator
  • GffMarker
  • GffType
  • GoogleBarChart
  • GoogleChartVenn
  • GoogleGenePercentBar
  • GoogleGeneRegionChart
  • GoogleGeneRegionNumExonsChart
  • GoogleHistogram
  • GoogleLineChart
  • GooglePlot
  • GooglePlotInt
  • GoTerm
  • GoTerms
  • Gpr
  • GprHtml
  • GprSeq
  • Gtex
  • GtexExperiment
  • Gtf2Marker
  • GuessTableTypes
  • HashLongLongArray
  • Hgvs
  • HgvsDna
  • HgvsProtein
  • HomHetStats
  • Hypergeometric
  • IdGenerator
  • IdMap
  • IdMapper
  • IdMapperEntry
  • IntegrationTest
  • Intergenic
  • IntergenicConserved
  • Interval
  • IntervalAndSubIntervals
  • IntervalComparatorByEnd
  • IntervalComparatorByStart
  • IntervalForest
  • IntervalNode
  • IntervalNodeOri
  • IntervalSetIterator
  • IntervalTree
  • IntervalTreeArray
  • IntervalTreeOri
  • IntHisto
  • Intron
  • IntronConserved
  • IntStats
  • Iterator2Iterable
  • Itree
  • IubString
  • Jaspar
  • KeyValue
  • LeadingEdgeFractionAlgorithm
  • LineChrPos
  • LineClassFileIterator
  • LineFileIterator
  • LineFilter
  • LineSeqFileIterator
  • Location
  • LocationTargetIsoform
  • LocationTargetIsoformInteraction
  • Log
  • Log.FatalErrorBehabiour
  • LogStats
  • LogStats.RequestResult
  • LossOfFunction
  • Marker
  • MarkerFileIterator
  • MarkerParentId
  • Markers
  • MarkerSeq
  • MarkerSerializer
  • MarkerTypes
  • MarkerUtil
  • MarkerWithFrame
  • MatrixEntry
  • MatrixEntryFileIterator
  • MicroCosmEntry
  • MicroCosmFileIterator
  • MicroRnaBindingSite
  • MineMarkerIntervals
  • MineTwoMarkerIntervals
  • Monitor
  • Motif
  • MotifFileIterator
  • MotifLogo
  • MultivalueHashMap
  • NeedlemanWunsch
  • NeedlemanWunschOverlap
  • NextProt
  • NextProtDb
  • NextProtHandler
  • NextProtMarkerFactory
  • NextProtSequenceConservation
  • NextProtXmlAnnotation
  • NextProtXmlEntry
  • NextProtXmlIsoform
  • NextProtXmlNode
  • Nmer
  • NmerCount
  • NmerCountWc
  • NoneAlgorithm
  • NormalDistribution
  • NullReader
  • ObservedOverExpected
  • ObservedOverExpectedCHG
  • ObservedOverExpectedCHH
  • ObservedOverExpectedCpG
  • OpenBitSet
  • OsCmdQueue
  • OsCmdRunner
  • OutputFormatter
  • Overlap
  • OverlapDnaSeq
  • OverlapFilter
  • OverlapFilterCompareAllAll
  • OverlapFilterDnaId
  • OverlapRessult
  • Parser
  • Pathway
  • Pcingola
  • PdbFile
  • PedEntry
  • PedFamily
  • PedFileIterator
  • PedGenotype
  • Pedigree
  • PedigreeEntry
  • PedPedigree
  • PlinkMap
  • Polymerisation
  • PosStats
  • Progress
  • PromoterSequences
  • ProteinInteractionLocus
  • ProteinProteinInteractionLocus
  • ProteinStructuralInteractionLocus
  • PurityChange
  • PvaluesList
  • Pwm
  • PwmAndSeqs
  • Qseq2Fastq
  • RandMarker
  • RankSumNoReplacementPdf
  • RankSumNoReplacementSimulate
  • RankSumPdf
  • RankSumPValueAlgorithm
  • RankSumPValueGreedyAlgorithm
  • RareAminoAcid
  • Reaction
  • Reaction.RegulationType
  • Reactome
  • ReadsOnMarkersModel
  • Regulation
  • RegulationBedFileIterator
  • RegulationConsensusMultipleBed
  • RegulationFileConsensus
  • RegulationFileIterator
  • RegulationFileSplitBytType
  • RegulationGffFileIterator
  • ReSampleInt
  • ReSampleMap
  • ReSampleMapRank
  • Result
  • SamEntry
  • SamFileIterator
  • SamHeader
  • SamHeaderRecord
  • SamHeaderRecordSq
  • SamplingStats
  • ScoreList
  • ScoreList.ScoreSummary
  • SeekableBufferedReader
  • SequenceComplexity
  • SequenceIndexer
  • SequenceReference
  • SequenceRotator
  • Sex
  • SmithWaterman
  • SnpEff
  • SnpEff.GeneDatabaseFormat
  • SnpEff.InputFormat
  • SnpEff.OutputFormat
  • SnpEffCmdAcat
  • SnpEffCmdBuild
  • SnpEffCmdBuildNextProt
  • SnpEffCmdCds
  • SnpEffCmdClosest
  • SnpEffCmdCount
  • SnpEffCmdDatabases
  • SnpEffCmdDownload
  • SnpEffCmdDump
  • SnpEffCmdDump.DumpFormat
  • SnpEffCmdEff
  • SnpEffCmdGenes2Bed
  • SnpEffCmdGsa
  • SnpEffCmdLen
  • SnpEffCmdPdb
  • SnpEffCmdProtein
  • SnpEffCmdSeq
  • SnpEffCmdShow
  • SnpEffCmdSpliceAnalysis
  • SnpEffCmdTranslocationsReport
  • SnpEffectPredictor
  • SnpEffPredictorFactory
  • SnpEffPredictorFactoryEmbl
  • SnpEffPredictorFactoryFeatures
  • SnpEffPredictorFactoryGenBank
  • SnpEffPredictorFactoryGenesFile
  • SnpEffPredictorFactoryGff
  • SnpEffPredictorFactoryGff2
  • SnpEffPredictorFactoryGff3
  • SnpEffPredictorFactoryGtf22
  • SnpEffPredictorFactoryKnownGene
  • SnpEffPredictorFactoryRand
  • SnpEffPredictorFactoryRefSeq
  • SpliceSite
  • SpliceSiteAcceptor
  • SpliceSiteBranch
  • SpliceSiteBranchU12
  • SpliceSiteDonor
  • SpliceSiteRegion
  • SpliceTypes
  • StreamGobbler
  • SubsequenceComparator
  • SuffixIndexerNmer
  • Svg
  • SvgBnd
  • SvgCds
  • SvgExon
  • SvgGene
  • SvgIntron
  • SvgNextProt
  • SvgScale
  • SvgSpacer
  • SvgTranscript
  • SvgTranslocation
  • TableFile
  • TestCasesAlign
  • TestCasesAnn
  • TestCasesAnnParse
  • TestCasesApplyDel
  • TestCasesApplyIns
  • TestCasesApplyMixed
  • TestCasesApplyMnp
  • TestCasesApplySnp
  • TestCasesBase
  • TestCasesBaseApply
  • TestCasesBinomial
  • TestCasesBuild
  • TestCasesCds
  • TestCasesChiSquare
  • TestCasesCircular
  • TestCasesCochranArmitage
  • TestCasesCodonTable
  • TestCasesCytoBands
  • TestCasesDel
  • TestCasesDels
  • TestCasesDnaNSequence
  • TestCasesDnaOverlap
  • TestCasesDnaSequence
  • TestCasesDnaSequenceByte
  • TestCasesEffectCollapse
  • TestCasesEffectCollapse2
  • TestCasesFasta
  • TestCasesFileIndexChrPos
  • TestCasesFisherExactTest
  • TestCasesGenePvalueList
  • TestCasesGenomicSequences
  • TestCasesGenotypeVector
  • TestCasesHgvs
  • TestCasesHgvsBase
  • TestCasesHgvsDnaDup
  • TestCasesHgvsDnaDupNegative
  • TestCasesHgvsExon
  • TestCasesHgvsIntron
  • TestCasesHgvsProtDup
  • TestCasesHypergeometric
  • TestCasesIns
  • TestCasesIntegrationAlphaFold
  • TestCasesIntegrationApply
  • TestCasesIntegrationBase
  • TestCasesIntegrationBuildPdb
  • TestCasesIntegrationCancer
  • TestCasesIntegrationCanonical
  • TestCasesIntegrationCircularGenome
  • TestCasesIntegrationCodingTag
  • TestCasesIntegrationConfig
  • TestCasesIntegrationCovid19
  • TestCasesIntegrationCutsomIntervals
  • TestCasesIntegrationDelEtc
  • TestCasesIntegrationDup
  • TestCasesIntegrationEff
  • TestCasesIntegrationEmbl
  • TestCasesIntegrationErrors
  • TestCasesIntegrationExonFrame
  • TestCasesIntegrationFilterTranscripts
  • TestCasesIntegrationGenBank
  • TestCasesIntegrationGenomicSequences
  • TestCasesIntegrationGff3
  • TestCasesIntegrationGtf22
  • TestCasesIntegrationHgvs
  • TestCasesIntegrationHgvsDel
  • TestCasesIntegrationHgvsDnaDup
  • TestCasesIntegrationHgvsFrameShift
  • TestCasesIntegrationHgvsHard
  • TestCasesIntegrationHgvsIns
  • TestCasesIntegrationHgvsLarge
  • TestCasesIntegrationHgvsMnps
  • TestCasesIntegrationHgvsUpDownStream
  • TestCasesIntegrationInsEtc
  • TestCasesIntegrationInsVep
  • TestCasesIntegrationLargeDeletion
  • TestCasesIntegrationLof
  • TestCasesIntegrationMarkerSeq
  • TestCasesIntegrationMissenseSilentRatio
  • TestCasesIntegrationMixedVariants
  • TestCasesIntegrationMnp
  • TestCasesIntegrationMotif
  • TestCasesIntegrationNextProt
  • TestCasesIntegrationNmd
  • TestCasesIntegrationNoChange
  • TestCasesIntegrationProtein
  • TestCasesIntegrationProteinInteraction
  • TestCasesIntegrationRefSeq
  • TestCasesIntegrationRegulation
  • TestCasesIntegrationSequenceOntology
  • TestCasesIntegrationSnp
  • TestCasesIntegrationSnpEff
  • TestCasesIntegrationSnpEffMultiThread
  • TestCasesIntegrationSnpEnsembl
  • TestCasesIntegrationSpliceRegion
  • TestCasesIntegrationStructural
  • TestCasesIntegrationTranscript
  • TestCasesIntegrationTranscriptError
  • TestCasesIntegrationVariant
  • TestCasesIntegrationVcfs
  • TestCasesIntegrationZzz
  • TestCasesIntergenic
  • TestCasesIntervals
  • TestCasesIntervalTree
  • TestCasesIntervalTreeArray
  • TestCasesIntervalTreeOri
  • TestCasesIntervalVariant
  • TestCasesIntStats
  • TestCasesIubString
  • TestCasesJaspar
  • TestCasesMarkerUtils
  • TestCasesMnps
  • TestCasesNextProt
  • TestCasesNmers
  • TestCasesOverlap
  • TestCasesProteinInteraction
  • TestCasesReactome
  • TestCasesSeekableReader
  • TestCasesSequenceIndexer
  • TestCasesSnps
  • TestCasesSpliceRegion
  • TestCasesSpliceSite
  • TestCasesStructuralDel
  • TestCasesStructuralDup
  • TestCasesStructuralInv
  • TestCasesStructuralTranslocations
  • TestCasesVariantDecompose
  • TestCasesVariantRealignment
  • TestCasesVcf
  • TestCasesZzz
  • TestGenome
  • TestSuiteIntegration
  • TestSuiteUnity
  • TfamEntry
  • Timer
  • Transcript
  • TranscriptSet
  • TranscriptSupportLevel
  • TranslocationReport
  • TsTvStats
  • Tuple
  • TxtSerializable
  • Upstream
  • Utr
  • Utr3prime
  • Utr5prime
  • Variant
  • Variant.VariantType
  • VariantBnd
  • VariantEffect
  • VariantEffect.Coding
  • VariantEffect.EffectImpact
  • VariantEffect.FunctionalClass
  • VariantEffectFilter
  • VariantEffectFusion
  • VariantEffects
  • VariantEffectStats
  • VariantEffectStructural
  • VariantFileIterator
  • VariantNonRef
  • VariantRealign
  • VariantStats
  • VariantTxtFileIterator
  • VariantTypeStats
  • VariantVcfEntry
  • VariantWithScore
  • VcfAnnotator
  • VcfAnnotatorChain
  • VcfConsequence
  • VcfConsequenceHeader
  • VcfEffect
  • VcfEntry
  • VcfEntry.AlleleFrequencyType
  • VcfFileIterator
  • VcfGenotype
  • VcfHapMapFileIterator
  • VcfHeader
  • VcfHeaderEntry
  • VcfHeaderFormat
  • VcfHeaderInfo
  • VcfHeaderInfo.VcfInfoNumber
  • VcfInfoType
  • VcfLof
  • VcfNmd
  • VcfOutputFormatter
  • VcfRefAltAlign
  • VcfStats
  • VersionCheck
  • Zzz