CHANGES IN VERSION 1.15.1
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Use BiocManager

CHANGES IN VERSION 1.13.5
-------------------------

BUG FIXES

    o Fixed an issue in plotCluster() on how it was loading the
        hg19IdeogramCyto object from the biovizBase package.

CHANGES IN VERSION 1.13.4
-------------------------

BUG FIXES

    o Fixed an issue with a call to GenomicRanges::gaps() that affected
        how the introns were plotting in plotRegionCoverage()
        when the underlying data has a specifying start and end of the
        chromosome (that is, a seqinfo() with seqlengths specified).
        Thanks to Emily Burke for reporting this issue
        https://github.com/emilyburke.


CHANGES IN VERSION 1.11.2
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Vignette now uses the new BiocStyle::html_document that was recently
        released.

CHANGES IN VERSION 1.7.10
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Help pages now document advanced arguments.

CHANGES IN VERSION 1.7.8
------------------------

BUG FIXES

    o Updated links to BrainSpan. Issue reported by Steve Semick
        https://github.com/SteveSemick.

CHANGES IN VERSION 1.7.1
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Dropped defunct functions.

CHANGES IN VERSION 1.5.8
------------------------

BUG FIXES

    o plotRegionCoverage() used to take into account the strand of the regions
        for finding transcripts that overlapped the regions. This was not a
        problem with DERs from derfinder since they have strand * by default
        but it is a problem when using it with stranded regions.
    o plotCluster() will also now ignore strand for finding neighboring regions.

CHANGES IN VERSION 1.5.4
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Only use distance if it's not NA in plotRegionCoverage()

CHANGES IN VERSION 1.3.4
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Dropped tMatrix() because it was a confusing plot and also lead to build
        errors.


CHANGES IN VERSION 1.3.3
------------------------

NEW FEATURES

    o Added the function tMatrix() which uses a GRanges object that has a 
        variable of interest to compute t-Statistics between bins of the genome.
        For each bin, the values of the variable of interest from the regions
        overlapping the bin are used. We use t-Statistics instead of correlation
        because not all bins will have the same number of regions. This type of
        plot is similar to interaction plots made for HiC data.

CHANGES IN VERSION 1.3.2
------------------------

NEW FEATURES

    o Added the vennRegions() function to visualize how many regions overlap
        known exons, introns, intergenic regions, none of them or several of 
        these groups.


CHANGES IN VERSION 1.3.1
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Deprecated functions with underscores in their names in favor of 
        camelCase functions. This was done to simplify the package.

CHANGES IN VERSION 1.1.6
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Adapted to work with bumphunter version >= 1.7.6

CHANGES IN VERSION 1.1.3
------------------------

BUG FIXES

    o Adapted plotCluster() and plotOverview() to derfinder 1.1.5


CHANGES IN VERSION 0.99.0
-------------------------

NEW FEATURES

    o Preparing to submit to Bioconductor.
    o Added tests and vignette.
    
SIGNIFICANT USER-VISIBLE CHANGES

    o plotOverview() and plotCluster() can now plot FWER adjusted p-values if
        calculated with derfinder::mergeResults()

CHANGES IN VERSION 0.0.4
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Hid some arguments in plotCluster() and plotOverview() as advanced just
        like in derfinder v0.0.74

BUG FIXES

    o Improved the speed in plotRegionCoverage() then 'txdb' is specified. Also
        fixed the introns on the gene track.

CHANGES IN VERSION 0.0.3
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o plotRegionCoverage() now has a 'txdb' argument. When specified, this 
        function will extract the transcript information needed and display
        the transcripts.


CHANGES IN VERSION 0.0.1
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Moved plotting functions from derfinder into this package