                       Changes in version 1.38.3                        

BUGFIXES

    o   Fix CpG islands read from UCSC database tables (hg38, mm10, mm39, rn6,
	  rn7, danRer10, danRer11, galGal5), and hg19 chromHMM states, which started
	  1 bp early because UCSC's 0-based starts were used as 1-based. CpG shores,
	  shelves, and inter-CGI regions, built from the islands, are fixed too.
	  Reported, with a fix, by Ryan Yancey (issue #54, PR #55).

                       Changes in version 1.38.2                        

BUGFIXES

    o   Fix plot_categorical() with the default fill = NULL, which failed when the
	  plot was drawn.

                       Changes in version 1.38.1                        

BUGFIXES

    o   Fix hg38_lncrna_gencode and mm10_lncrna_gencode, which failed after
	  AnnotationHub removed its GENCODE resources (AH75123, AH49550). All lncRNA
	  annotations are now downloaded from GENCODE over HTTPS, using the same
	  releases as before (hg19: 19, hg38: 31, mm10: M6).

                       Changes in version 1.16.0                        

USER-FACING CHANGES

    o   Export expand_annotations(), tidy_annotations(), and subset_order_tbl().

BUGFIXES

    o   Fix incorrect shortcut search for HMMs.

                        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.
