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annotatr 1.38.3

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).

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

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).

Add the ability to facet over two variables in plot_numerical().
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_().
Make TxDb and OrgDb packages Suggests instead of Imports. NOTE: This saves space, but also requires downloading the appropriate packages as needed.
Add list_env() function to the annotatr_cache environment to see what custom annotations have been read in and added to the cache.

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

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

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

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

annotatr is a package to quickly and flexibly annotate genomic regions to genomic annotations.
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.
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.
Annotations are currently available for hg19, mm9, mm10, dm3, dm6, rn4, rn5, and rn6. Any species is supported through custom annotations.
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.
Annotations are determined via GenomicRanges::findOverlaps(), and all annotations are returned, rather than imposing a prioritization.
annotatr provides several helpful summarization (using dplyr) and plot functions (using ggplot2) to investigate trends in data associated with the genomic regions over annotations.