analyze_tf_cobinding    Analyze statistical significance of TF
                        co-binding at enhanceosome regions
analyze_tf_overlap      Analyze pairwise and multi-way overlap between
                        transcription factor binding sites
annotate_enhancers      Annotate putative enhancers with functional
                        database overlaps
annotations             Access the genomic annotations slot of an
                        epiRomicsS4 object
annotations-set         Replace the annotations slot of an epiRomicsS4
                        object
benchmark_enhancer_predictor
                        Evaluate histone marks against any curated
                        reference database
build_database          Build epiRomics database
cache_data              Download and Cache epiRomics Example Data
call_accessible_regions
                        Compute per-region signal z-scores from a
                        BigWig file
chromatin_state_categories
                        Return chromatin state category definitions
classify_celltype_accessibility
                        Classify regions by cell-type-specific binary
                        accessibility
classify_chromatin_states
                        Classify genomic regions by histone chromatin
                        state with genomic context
epiRomics-package       epiRomics: Epigenomic Analysis Package Built
                        for R (epiRomics)
epiRomicsS4-accessors   Accessors for the epiRomicsS4 class
epiRomicsS4-class       An S4 class to manage epiRomics databases and
                        downstream results
filter_accessible_regions
                        Filter putative enhancers by chromatin
                        accessibility evidence
filter_enhancers        Filters putative enhancers called by
                        epiRomics_enhancers by crossing against curated
                        FANTOM data
find_enhanceosomes      Identifies putative enhanceosome regions by
                        cross-referencing candidate enhancer regions
                        against co-TF enrichment
find_enhancers_by_comarks
                        Identifies putative enhancer regions utilizing
                        select histone mark co-occurrence
find_putative_enhancers
                        Identify putative enhancer regions using
                        rule-based histone logic
genome                  Access the genome assembly name
genome-set              Replace the genome assembly name
get_cache_path          Get Path to Cached epiRomics Data (No Download)
get_regions_of_interest
                        Define regions of interest and filter
                        enhanceosome by overlap
has_cache               Check Whether epiRomics Example Data is Cached
make_example_bigwig     Create a temporary synthetic BigWig file for
                        use in examples
make_example_database   Build a synthetic epiRomicsS4 database for use
                        in examples
make_example_enhanceosome
                        Build a synthetic enhanceosome result for use
                        in examples
make_example_putative_enhancers
                        Build a synthetic putative-enhancer result for
                        use in examples
maxCovBwCached          BigWig coverage calculation
maxCovFilesCached       Multiple BigWig coverage calculation
meta                    Access the metadata slot of an epiRomicsS4
                        object
meta-set                Replace the metadata slot of an epiRomicsS4
                        object
organism                Access the organism annotation package name
organism-set            Replace the organism annotation package name
plot_gene_tracks        Visualize any gene locus with multi-track
                        BigWig overlay
plot_quick_view         Quick standalone gene/region visualization from
                        BigWig files
plot_signal_histogram   Plot signal distribution histogram for
                        accessibility threshold selection
plot_tracks             Multi-track genomic visualization (base R
                        graphics)
txdb                    Access the TxDb package::object identifier slot
txdb-set                Replace the TxDb identifier slot of an
                        epiRomicsS4 object
