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.