All Classes
AndersonDarling
AndersonDarling.IS_DATA_NORMALIZED
AssociatingPcasWithAnnotation
AUC
BaseAnnot
BeagleImputedToTriTyper
BedEntry
BedFile
BedGraphEntry
BedGraphFile
BinaryFile
BinaryGZipFloatMatrix
BinaryInteractionCohort
BinaryInteractionCovariateIterator
BinaryInteractionFile
BinaryInteractionFileConstructorBuilder
BinaryInteractionFileCreator
BinaryInteractionFileException
BinaryInteractionGene
BinaryInteractionGeneAbstract
BinaryInteractionGeneCreator
BinaryInteractionGeneStatic
BinaryInteractionQtlZscores
BinaryInteractionQueryResult
BinaryInteractionVariant
BinaryInteractionVariantAbstract
BinaryInteractionVariantCreator
BinaryInteractionVariantStatic
BinaryInteractionZscores
BinaryResultDataset
BinaryResultProbe
BinaryResultProbeSummary
BinaryResultSNP
BinaryResultSNPSummary
Binning
BufferedSNPLoader
CheckAssocationMultipleGeneProbes
CheckMatrixForValidBetaValues
ChiSquare
ChrAnnotation
Chromosome
ChrPosMap
ChrPosTreeMap
CompareAllelicDirections
ConcurrentCorrelation
ConcurrentCorrelationTask
ConcurrentCovariation
ConcurrentCovariationTask
ConsoleGUIElems
ConvertBetaAndMvalues
ConvertDoubleMatrixDataToTriTyper
ConverteUandMTo
Correlation
CubicSpline
DeepCopy
Demographics
Dependifier
Descriptives
DetermineLD
DoubleMatrixDataset
DoubleMatrixDataset
DoubleMatrixDatasetAC
DoubleMatrixDatasetAC.LoadLabels
DoubleMatrixDatasetRA
DoubleParseTask
EQTL
Exon
ExpressionDataset
FDRUtils
FDRUtils.AbsoluteValues
FDRUtils.CloneArrays
FDRUtils.SortArrays
Features
FinalReportToTriTyper
FisherExactTest
Fmath
ForestPlot
ForestPlot.Output
Gene
GenomicBoundaries
GenomicBoundariesIterator
GenomicBoundariesSimple
GenomicBoundary
GenomicRange
GffAttributeFilter
GffElement
GffElementIterator
GffReaderInterface
GMTFile
Goniometry
Gpio
GtfReader
GWASCatalog
GWASLocus
GWASPublication
GWASSNP
GWASTrait
HashingInputStream
HashingOutputStream
Heatmap
Heatmap.Output
Heterogeneity
HWE
ImputeImputedToTriTyperV2
Independifier
InplaceArrayQuickSort
IntervalTree
InversionCallsToTriTyper
KolmogorovSmirnov
LargeByteArray
Log2Transform
MachImputedToTriTyper
MachImputedTransposedDosageToTriTyper
MatrixHandling
MatrixHandling
MatrixTools
MatrixTools
MergeDoubleMatrices
MergeDoubleMatrices
MethylationAssociatoingAnnotationWithValues
MinimacImputedToTriTyper
MultiThreadedInPlaceQuickSort
NetworkConverter
Normalization
Pair
Pair.SORTBY
ParseSoftFile
ParseTcgaMethylationFile
ParseTextTable
PCA
PeakFile
PeakFile.PEAKFORMAT
PedAndMapToTriTyper
PerChrIntervalTree
PileupEntry
PileupFile
PileupParseException
PileupToVcf
Primitives
ProbeAnnotation
ProbeAnnotation
ProbeTranslation
ProgressBar
QTLTextFile
QuantileNormalization
QValues
QValues.SMOOTHER
RandomAccessFile
Range
RangeEndReverseComparator
RangeStartComparator
RankArray
RankDoubleArray
RankIntArray
reading
ReferenceGenomeFasta
Regression
RegulomeDbEntry
RegulomeDbFile
RegulomeDbFiles
RegulomeDbIterator
RegulomeDbSupportingData
RunTimer
RunTimer.Granularity
ScatterPlot
ScatterPlot.OUTPUTFORMAT
SmoothSort
SNP
SNPAnnotation
SNPLoader
SoftfileAnnotation
SortableSNP
SortableSNP.SORTBY
StringDoubleObject
StringDoubleObjectSorterSortOnDouble
StringIntegerObject
StringIntegerObjectSorterSortOnInteger
StringRange
Strings
SymmetricByteDistanceMatrix
SymmetricShortDistanceMatrix
TestGffIntervalTree
TextFile
TheilSen
Transcript
Triple
TriTyperConcatDatasets
TriTyperExpressionData
TriTyperGeneticalGenomicsDataset
TriTyperGeneticalGenomicsDatasetSettings
TriTyperGenotypeData
TriTyperGenotypeDataMerger
TriTyperReferenceConcordantPedAndMapExporter
TriTyperSNPMappings
TriTyperToDosageConverter
TriTyperToMachImputedTransposed
TriTyperToPedAndMapConverter
TriTyperToPlinkDosage
TriTyperToTabSeparated
TriTyperToVCF
TTest
TwoStepLeastSquares
UCSCDataObject
UCSCDataObject.SORTBY
UCSCTrack
VariantAnnotator
VCFToTriTyper
VectorSorter
VennDiagram
ViolinBoxPlot
ViolinBoxPlot.Output
WGAFileMatrixGenotype
WGAFileMatrixImputedDosage
WGAFileMatrixRawData
WigFile
WigFile.STEPMODE
WilcoxonMannWhitney
ZScores