assign_peak_segments    Assign whole peaks to all overlapping defined
                        gene loci.
assign_peaks            Assign peak midpoints to defined gene loci.
broadenrich             Run Broad-Enrich on broad genomic regions
calc_peak_gene_overlap
                        Add peak overlap and ratio to result of
                        'num_peaks_per_gene()'
chipenrich              Run ChIP-Enrich on narrow genomic regions
chipenrich_package      chipenrich: Gene Set Enrichment For ChIP-seq
                        Peak Data
filter_genesets         Function to filter genesets by locus definition
                        and size
genome_to_organism      Get the correct organism code based on genome
genome_to_orgdb         Get Entrez ID to gene symbol mappings for
                        custom locus definitions
get_test_method         Get the test function name from the method name
load_peaks              Convert a BEDX+Y data.frame and into GRanges
num_peaks_per_gene      Aggregate peak assignments over the 'gene_id'
                        column
plot_chipenrich_spline
                        QC plot for ChIP-Enrich
plot_dist_to_tss        Plot histogram of distance from peak to nearest
                        TSS
plot_gene_coverage      QC plot for Broad-Enrich
plot_polyenrich_spline
                        QC plot for Poly-Enrich
polyenrich              Run Poly-Enrich on narrow genomic regions
post_process_enrichments
                        Post process the 'data.frame' of enrichment
                        results
postprocess_peak_grs    A helper function to post-process peak GRanges
read_bed                Read files containing peaks or genomic regions
read_geneset            Function to read custom gene sets from file
read_ldef               Function to read custom locus definition from
                        file
read_mappa              Function to read custom mappability files
recode_peaks            Recode a vector of number of peaks to binary
                        based on threshold
reset_ncores_for_windows
                        Reset n_cores for Windows
setup_genesets          Function to setup genesets
setup_locusdef          Function to setup locus definitions
setup_mappa             Function to setup mappability
supported_genesets      Display supported genesets for gene set
                        enrichment.
supported_genomes       Display supported genomes.
supported_locusdefs     Display supported locus definitions
supported_methods       Display supported gene set enrichment methods.
supported_read_lengths
                        Display supported read lengths for mappability
