Version: 1.5.3
Category: NEW FEATURES
Text: Integration with the new InteractionSet package provides new
        features including more overlaps methods and conversion to
        other classes for storing genomic interaction data. See
        InteractionSet documentation for more details.

Version: 1.5.3
Category: SIGNIFICANT USER-LEVEL CHANGES
Text: Following InteractionSet integration, distance calculation is
        done differently and some distances may differ by 1bp.

Version: 1.5.3
Category: DEPRECATED AND DEFUNCT
Text: 'annotateAnchors' is deprecated and replaced by
        'annotateRegions'.

Version: 1.1.0
Category: NEW FEATURES
Text: Import method for reading data from two bam files containing
        paired end reads.

Version: 1.1.0
Category: NEW FEATURES
Text: A function for removing duplicate interactions: 'removeDups'

Version: 1.1.0
Category: NEW FEATURES
Text: Two methods for finding probable distance cutoffs for self
        ligations: 'get_binom_ligation_threshold' and
        'get_self_ligation_threshold'.

Version: 1.1.0
Category: NEW FEATURES
Text: 'countsBetweenAnchors': a function to summarise interactions
        between a set of genomic regions of interest.

Version: 1.1.0
Category: SIGNIFICANT USER-LEVEL CHANGES
Text: GenomicInteractions objects have been refactored for consistency
        with GRanges objects. Interaction-level metadata such as
        p-values is now stored as a DataFrame accessible using 'mcols'.

Version: 1.1.0
Category: SIGNIFICANT USER-LEVEL CHANGES
Text: importing data from a file is now done using
        'makeGenomicInteractionsFromFile'

Version: 1.1.0
Category: SIGNIFICANT USER-LEVEL CHANGES
Text: 'GenomicInteractions' can be used to construct a new object from
        anchors as GRanges objects and metadata.

Version: 1.1.0
Category: SIGNIFICANT USER-LEVEL CHANGES
Text: 'show' method looks nicer and is faster.

Version: 1.1.0
Category: DEPRECATED AND DEFUNCT
Text: 'FDR', 'pValue', 'normalisedCounts', 'genomeName': no longer
        needed because of refactoring. Access metadata by 'mcols'
        instead.

Version: 1.1.0
Category: DEPRECATED AND DEFUNCT
Text: 'count' renamed to 'interactionCounts'

Version: 1.1.0
Category: BUG FIXES
Text: