Changes in version 1.21.4                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Documentation website is now available at
    http://leekgroup.github.io/derfinderPlot/. It gets updated with
    every commit on the master branch (bioc-devel) using GitHub Actions
    and pkgdown.

                       Changes in version 1.21.3                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Code in all examples has been re-styled thanks to
    styler::style_pkg(), see dev/02_update.R for details.

                       Changes in version 1.21.2                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Switched from Travis to GitHub actions through usethis.
  - Build the documentation website automatically with pkgdown.
  - Added a dev/01_setup.R script.
  - Now using a README.Rmd file.

                       Changes in version 1.21.1                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Use GenomeInfoDb::getChromInfoFromUCSC() when possible instead of
    data from biovizBase::hg19Ideogram for getting the hg19 chromosome
    lengths.

                       Changes in version 1.19.3                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Added a NEWS.md file to track changes to the package.

                       Changes in version 1.17.2                        

NEW FEATURES

  - Add ORCID's following changes at
    http://bioconductor.org/developers/package-guidelines/#description

                       Changes in version 1.15.1                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Use BiocManager

                       Changes in version 1.13.5                        

BUG FIXES

  - 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

  - 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 E
    Burke for reporting this issue https://github.com/emilyburke.

                       Changes in version 1.11.2                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Vignette now uses the new BiocStyle::html_document() that was
    recently released.

                       Changes in version 1.7.10                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Help pages now document advanced arguments.

                        Changes in version 1.7.8                        

BUG FIXES

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

                        Changes in version 1.7.1                        

SIGNIFICANT USER-VISIBLE CHANGES

  - Dropped defunct functions.

                        Changes in version 1.5.8                        

BUG FIXES

  - 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.
  - plotCluster() will also now ignore strand for finding neighboring
    regions.

                        Changes in version 1.5.4                        

SIGNIFICANT USER-VISIBLE CHANGES

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

                        Changes in version 1.3.4                        

SIGNIFICANT USER-VISIBLE CHANGES

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

                        Changes in version 1.3.3                        

NEW FEATURES

  - 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

  - 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

  - 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

  - Adapted to work with bumphunter version >= 1.7.6

                        Changes in version 1.1.3                        

BUG FIXES

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

                       Changes in version 0.99.0                        

NEW FEATURES

  - Preparing to submit to Bioconductor.
  - Added tests and vignette.

SIGNIFICANT USER-VISIBLE CHANGES

  - 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

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

BUG FIXES

  - 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

  - 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

  - Moved plotting functions from derfinder into this package