annotate_regions        A function to intersect user region data with
                        annotation data
annotations             example_annotations data
annotatr                annotatr: Annotation of Genomic Regions to
                        Functional Annotations
annotatr_cache          A global-variable to hold custom annotations
                        loaded in an R session
build_ah_annots         A helper function to build arbitrary
                        annotatinos from AnnotationHub
build_annotations       A function to build annotations from TxDb.* and
                        AnnotationHub resources
build_ccre_annots       A helper function to build ENCODE cCRE
                        annotations.
build_cpg_annots        A helper function to build CpG related
                        annotations.
build_enhancer_annots   A helper function to build enhancer annotations
                        for hg19 and mm10 from FANTOM5.
build_gene_annots       A helper function to build genic annotations.
build_hmm_annots        A helper function to build chromHMM annotations
                        for hg19 from UCSC Genome Browser.
build_lncrna_annots     A helper function to build lncRNA annotations.
build_mane_txdb         Function to build a TxDb of the MANE Select
                        transcripts
build_txdb_annotations
                        Build gene annotations from any TxDb or EnsDb
build_txdb_gene_annots
                        A helper function to build genic annotations
                        from a TxDb or EnsDb
builtin_annotations     Function listing which annotations are
                        available.
builtin_annotations_table
                        Table of builtin annotations by genome
builtin_genomes         Function returning supported TxDb.* genomes
cached-annotations      Cached annotations
check_annotations       Function to check for valid annotations
check_regions_genome    Function to check regions and annotations are
                        from the same genome
clear_cached_annotations
                        Clear cached annotations and downloads
coannotation_pairs      Function to find the pairs of annotation types
                        on each region
download_annotation_file
                        Function to download a file, with retries, into
                        the cache
expand_annotations      Function to expand annotation shortcuts
get_annotation_rname    Function to get the cache resource name of a
                        built annotation
get_bfc                 Function to get the BiocFileCache for the cache
get_cache_dir           Function to get the directory of the cache
get_cache_rids          Function to get the resource IDs of cache
                        entries
get_cellline_from_code
                        Function to return cell line from chromatin
                        annotation code
get_cellline_from_shortcut
                        Function to return cell line from chromatin
                        annotation shortcut
get_chrom_aliases       Function to map any chromosome alias of a
                        genome to its UCSC-style name
get_genark_seqinfo      Function to get the Seqinfo of a GenArk genome
                        with UCSC-style names
get_genark_url          Function to get the URL of a file in the UCSC
                        GenArk hub for a genome
get_gene_table          Function to map gene IDs to gene symbols,
                        Entrez IDs, and Ensembl IDs
get_mane_summary        Function to get the MANE Select summary
get_orgdb_name          Function to get correct org.* package name
                        based on genome
get_txdb_name           Function to get correct TxDb.* package name
                        based on genome
list_cached_annotations
                        List cached annotations and downloads
load_cached_annotation
                        Function to load a built annotation from the
                        cache
plot_annotation         Plot the number of regions per annotation
plot_categorical        Plot a categorical data variable over another
plot_coannotations      Plot pair-wise annotations across regions
plot_numerical          Plot numerical data over regions or regions
                        summarized over annotations
plot_numerical_coannotations
                        Plot numerical data occurring in pairs of
                        annotations
randomize_regions       Randomize Regions
read_annotations        Read custom annotations
read_ccre_bed           Function to read an ENCODE cCRE registry BED
                        file
read_regions            Read genomic regions in BEDX+Y format
reformat_hmm_codes      Function to recode classes from chromHMM type
                        column
save_cached_annotation
                        Function to save a built annotation in the
                        cache
set_genome_seqinfo      Function to give a GRanges the seqinfo of a
                        genome
standardize_mcols       Function to give an annotation the standard
                        mcols
strip_id_version        Function to remove the version from Ensembl IDs
subset_order_tbl        Function to subset a tbl_df or grouped_df by a
                        column
summarize_annotations   Summarize annotation counts
summarize_categorical   Summarize categorical data over groupings of
                        annotated regions
summarize_genes         Summarize annotated regions by gene
summarize_numerical     Summarize numerical data over groupings of
                        annotated regions
tidy_annotations        Function to tidy up annotation accessors for
                        visualization
ucsc_seqlevels          Function to rename sequences to UCSC-style
                        names
