CHANGES IN VERSION 1.6.0
------------------------

NEW FEATURES

  o Add support for chicken (galGal5).

USER-FACING CHANGES

  o Add the ability to facet over two variables in plot_numerical().
  o Add the ability to keep duplicate regions in summarize_categorical() and
    plot_categorical(). This is accomplished with the 'by' parameter in the
    former and by the 'x' and 'fill' parameters in the latter, and passing
    their contents into the '.dots' parameter of dplyr::distinct_().
  o Make TxDb and OrgDb packages Suggests instead of Imports. NOTE: This saves
    space, but also requires downloading the appropriate packages as needed.
  o Add list_env() function to the annotatr_cache environment to see what
    custom annotations have been read in and added to the cache.

BUGFIXES

  o Replace dplyr::summarize_each_() with dplyr::summarize_at() in line with
    deprecation in the dplyr package.
  o Prefix builtin_ functions with annotatr:: so that packages that Import
    annotatr don't encounter errors.

CHANGES IN VERSION 1.2.0
------------------------

NEW FEATURES

  o Add support for CpG annotations for hg38, mm10, and rn6 via the UCSC goldenpath URLs.
  o Add a function to build annotations from AnnotationHub resources, build_ah_annots().
  o Add support for chromHMM tracks (chromatin state) from the UCSC Genome Browser.
    o Users may annotate to chromatin states in multiple cell lines, if desired.
  o Use rtracklayer::liftOver to lift hg19 and mm9 enhancers into hg38 and mm10.

USER-FACING CHANGES

  o Add minoverlaps parameter to annotate_regions() that is passed to
    GenomicRanges::findOverlaps().
  o Change supported_annotations() and supported_genomes() into builtin_annotations()
    and builtin_genomes(). This enables more flexibility required for AnnotationHub
    annotations.
  o Added documentation for coercing result of annotate_regions() to data.frame
     and subsetting based on gene symbol to the vignette.

BUGFIXES

  o Fixed a bug in coercion of GRanges to data.frame where row.names could be
    duplicated. Thanks to @kdkorthauer.
  o Require GenomeInfoDb >= 1.10.3 because of changes to NCBI servers.
  o Change scale_fill_brewer() to scale_fill_hue() in plot_categorical() to enable
    more categories and avoid plotting abnormalities.
  o Fixed bug that mistakenly displayed some supported annotations.
  o Fixed a bug in lncRNA annotation building caused by incomplete reference.

CHANGES IN VERSION 0.99.13
--------------------------

PKG FEATURES

  o annotatr is a package to quickly and flexibly annotate genomic regions to
    genomic annotations.

    o Genomic annotations include CpG features (island, shore, shelves, and
	  open sea), genic features (1-5kb upstream of TSS, promoters,
	  5'UTRs, exons, introns, CDS, 3'UTRs, intron/exon boundaries, and exon/
	  intron boundaries), as well as enhancers from the FANTOM5 consortium for
	  hg19 and mm9.

	  o Annotations are built at runtime using the TxDb.*, AnnotationHub, and
	    rtracklayer packages. Users can select annotations a la carte, or via
		shortcuts, such as hg19_basicgenes.

	  o Annotations are currently available for hg19, mm9, mm10, dm3, dm6, rn4,
	    rn5, and rn6. Any species is supported through custom annotations.

  o Genomic regions are read in using the rtracklayer::import() function, and
    the extraCols argument enables users to include an arbitrary number of
	categorical or numerical data with the genomic regions.

  o Annotations are determined via GenomicRanges::findOverlaps(), and all
    annotations are returned, rather than imposing a prioritization.

  o annotatr provides several helpful summarization (using dplyr) and plot
    functions (using ggplot2) to investigate trends in data associated with the
	genomic regions over annotations.
