HiCDOC                  Default pipeline to run on the HiCDOC analysis.
HiCDOC-package          A/B compartment detection and differential
                        analysis
HiCDOCDataSet-class     'HiCDOCDataSet' S4 class.
HiCDOCDataSet-methods   Methods to access a 'HiCDOCDataSet' components.
HiCDOCDataSet-parameters
                        Access the parameters of a 'HiCDOCDataSet'.
HiCDOCDataSetFromCool   'HiCDOCDataSet' constructor from Cool files.
HiCDOCDataSetFromHiC    'HiCDOCDataSet' constructor from HiC files.
HiCDOCDataSetFromHiCPro
                        'HiCDOCDataSet' constructor from HiC-Pro files.
HiCDOCDataSetFromTabular
                        'HiCDOCDataSet' constructor from a tabular
                        file.
detectCompartments      A and B compartments detection and differences
                        across conditions.
exampleHiCDOCDataSet    Example HiCDOCDataSet.
exampleHiCDOCDataSetProcessed
                        Example HiCDOCDataSet, filtered, normalized and
                        with compartements detected.
filterSmallChromosomes
                        Filter small chromosomes.
filterSparseReplicates
                        Filter sparse replicates.
filterWeakPositions     Filter weak positions.
normalizeBiologicalBiases
                        Normalize biological biases.
normalizeDistanceEffect
                        Normalize distance effect.
normalizeTechnicalBiases
                        Normalize technical biases.
plotCentroids           Plot centroids.
plotCompartmentChanges
                        Plot compartment changes.
plotCompartments        Plot A/B compartments.
plotConcordanceDifferences
                        Plot the distribution of concordance
                        differences.
plotConcordances        Plot concordances.
plotDistanceEffect      Plot the distance effect.
plotInteractions        Plot interaction matrices.
plotSelfInteractionRatios
                        Plot boxplots of self interaction ratios.
reduceHiCDOCDataSet     Reduce a 'HiCDOCDataSet'.
