HiCDOC-package	HiCDOC-package
chromosomes	HiCDOCDataSet-methods
chromosomes,HiCDOCDataSet-method	HiCDOCDataSet-methods
compartments	HiCDOCDataSet-methods
compartments,HiCDOCDataSet-method	HiCDOCDataSet-methods
concordances	HiCDOCDataSet-methods
concordances,HiCDOCDataSet-method	HiCDOCDataSet-methods
defaultHiCDOCParameters	HiCDOCDataSet-parameters
detectCompartments	detectCompartments
differences	HiCDOCDataSet-methods
differences,HiCDOCDataSet-method	HiCDOCDataSet-methods
exampleHiCDOCDataSet	exampleHiCDOCDataSet
exampleHiCDOCDataSetProcessed	exampleHiCDOCDataSetProcessed
filterSmallChromosomes	filterSmallChromosomes
filterSparseReplicates	filterSparseReplicates
filterWeakPositions	filterWeakPositions
HiCDOC	HiCDOC
HiCDOCDataSet	HiCDOCDataSet-class
HiCDOCDataSet-class	HiCDOCDataSet-class
HiCDOCDataSet-methods	HiCDOCDataSet-methods
HiCDOCDataSet-parameters	HiCDOCDataSet-parameters
HiCDOCDataSetFromCool	HiCDOCDataSetFromCool
HiCDOCDataSetFromHiC	HiCDOCDataSetFromHiC
HiCDOCDataSetFromHiCPro	HiCDOCDataSetFromHiCPro
HiCDOCDataSetFromTabular	HiCDOCDataSetFromTabular
normalizeBiologicalBiases	normalizeBiologicalBiases
normalizeDistanceEffect	normalizeDistanceEffect
normalizeTechnicalBiases	normalizeTechnicalBiases
parameters	HiCDOCDataSet-parameters
parameters,HiCDOCDataSet-method	HiCDOCDataSet-parameters
parameters<-	HiCDOCDataSet-parameters
parameters<-,HiCDOCDataSet-method	HiCDOCDataSet-parameters
plotCentroids	plotCentroids
plotCompartmentChanges	plotCompartmentChanges
plotCompartments	plotCompartments
plotConcordanceDifferences	plotConcordanceDifferences
plotConcordances	plotConcordances
plotDistanceEffect	plotDistanceEffect
plotInteractions	plotInteractions
plotSelfInteractionRatios	plotSelfInteractionRatios
reduceHiCDOCDataSet	reduceHiCDOCDataSet
sampleConditions	HiCDOCDataSet-methods
sampleConditions,HiCDOCDataSet-method	HiCDOCDataSet-methods
sampleReplicates	HiCDOCDataSet-methods
sampleReplicates,HiCDOCDataSet-method	HiCDOCDataSet-methods
show,HiCDOCDataSet-method	HiCDOCDataSet-methods
_PACKAGE	HiCDOC-package
