Changes in version 1.8.0:

    o   Streamlined filterDirect(), filterTrended(), and added tests for
	 them. Also allowed specification of which assay to use for the data
	 and reference objects.

    o   enrichedPairs() and neighborCounts() now return counts for
	 neighbourhood regions, not just the enrichment values.

    o   filterPeaks() will compute (and optionally return) enrichment values
	 from neighbourhood counts.

    o   normalizeCNV() and correctedContact() allow specification of which
	 assay matrix to use from the SE objects.

    o   Refactored a great deal of the C++ code for improved clarity.

    o   Overhauled handling of DNase Hi-C data, so that pseudo-fragments are
	 no longer necessary. Most functions now automatically recognise
	 DNase-C data from an empty GRanges in param$fragments.  Deprecated
	 segmentGenome() and prepPseudoPairs(), added the emptyGenome()
	 function.

    o   Updated user's guide.

Changes in version 1.6.0:

    o   Relaxed checks in preparePairs(), prepPseudoPairs() when more
	 chromosomes are supplied than needed.

    o   Relaxed checks in connectCounts() when extra chromosomes are in the
	 input ranges.

    o   Fixed an issue with preparePairs() when too many file handles are
	 open.

    o   Fixed clash between BiocGenerics and Matrix which().

    o   Modified domainDirections() to return a RangedSummarizedExperiment.

    o   Removed defunct DIList class and methods.

    o   Switched from seqlevels() to seqlevelsInUse() for fragment
	 intervals.

    o   Updated user's guide, documentation.

Changes in version 1.4.0:

    o   Deprecated DIList objects and methods in favour of InteractionSet
	 objects.

    o   marginCounts() now returns a RangedSummarizedExperiment for all
	 bins.

    o   Added the max.height argument to the rotPlaid() and rotDI()
	 functions.

    o   Added the diClusters() function for post-hoc cluster-level FDR
	 control.

    o   Added the annotatePairs() function for convenient annotation of
	 (clusters of) interactions.

    o   Fixed a bug in plotPlaid() when the interaction space was empty.

    o   Fixed a bug in preparePairs() where unmapped chimeric segments led
	 to the loss of the entire pair.

    o   Updated user's guide, documentation and tests.

Changes in version 1.2.0:

    o   Renamed normalize() to normOffsets().

    o   Added library size specification to DIList methods normOffsets(),
	 asDGEList().

    o   Fixed bugs under pathological settings in plotPlaid(), plotDI(),
	 rotPlaid(), rotDI().

    o   Optimized C++ code for connectCounts(), squareCounts().

    o   Streamlined various R utilities used throughout all functions.

    o   Added iter_map.py to inst/python, for iterative mapping of DNase
	 Hi-C data.

    o   Added the neighborCounts() function, for simultaneous read counting
	 and enrichment calculation.

    o   Added exclude for enrichedPairs(), to provide an exclusion zone in
	 the local neighborhood.

    o   Switched default colour in rotPlaid(), plotPlaid() to black.

    o   Added compartmentalize() function to identify genomic compartments.

    o   Added domainDirections() function to help identify domains.

    o   Modified correctedContact() to allow distance correction and report
	 factorized probabilities directly.

    o   Modified marginCounts() function for proper single-end-like
	 treatment of Hi-C data.

    o   Extended clusterPairs() to merge bin pairs from multiple DILists.

    o   Switched to reporting ranges directly from boxPairs(), added support
	 for minimum bounding box output.

    o   Modified consolidatePairs() to accept index vectors for greater
	 modularity.

    o   Added reference argument for large bin pairs, in filterDirect() and
	 filterTrended().

    o   Added filterDiag() convenience function for filtering of
	 (near-)diagonal bin pairs.

    o   Slight change to preparePairs() diagnostic reports when dedup=FALSE,
	 and for unpaired reads.

    o   Added option for a distance-based threshold to define invalid
	 chimeras in preparePairs().

    o   Updated documentation, tests and user's guide.

    o   Added diffHic paper entry to CITATION.

Changes in version 1.0.0:

    o   New package diffHic, for detection of differential interactions from
	 Hi-C data.