.add_tss_annotation     Add TSS annotation to peaks
.parse_input_diff       Parses input data of various types (e.g., named
                        lists of 'GRanges' or 'data.frame', or a
                        'GRangesList') into a single tidy 'data.frame',
                        with a 'cell_type' column.
.standardize_peaks      Standardizes peak input, ensuring that input
                        peaks is a 'GRanges' object, removes alternate
                        scaffolds ('_alt', 'random', 'fix', 'Un'), and
                        assigns region IDs as names.
SPICEY                  SPICEY: Tissue specificity analysis for
                        single-cell data The SPICEY package provides a
                        user-friendly pipeline for quantifying and
                        visualizing tissue specificity specificity from
                        single-cell ATAC-seq and/or single cell RNA-seq
                        datasets, typically processed with tools such
                        as Seurat or Signac. The core outputs of SPICEY
                        are two tissue specific metrics, combined with
                        entropy-based measures.
annotate_with_coaccessibility
                        Annotate peaks with co-accessible genes using
                        Cicero links
annotate_with_nearest   Annotates regulatory elements (e.g., ATAC-seq
                        peaks) to the nearest gene
atac                    Example single-cell ATAC-seq differential
                        accessibility data
cicero_links            Example Cicero co-accessibility links
compute_spicey_index    Compute cell type specificity scores from
                        single-cell RNA and/or ATAC data
entropy_index           Calculate normalized Shannon-entropy of
                        specificity scores
extract_gene_peak_annotations
                        Overlap peaks with gene promoters to obtain
                        gene annotations
get_promoters           Extract promoter regions annotated gene symbols
                        from a TxDb and AnnotationDbi object
link_spicey             Link RETSI regions to GETSI scores using
                        gene-based association methods
plot_heatmap            Plot a SPICEY score gene-by-cell-type heatmap
prepare_heatmap_data    Prepare data for SPICEY heatmap
rna                     Example single-cell RNA-seq differential
                        expression data
specificity_index       Calculate specificity scores for grouped
                        features
spicey_heatmap          SPICEY heatmap for gene specificity across cell
                        types
