DamIDResults-class      The DamIDResults Class
analyse_go_enrichment   Perform Gene Ontology (GO) enrichment analysis
                        for differentially bound/expressed regions
analysisTable           Access the differential binding analysis
                        results
browse_igv_regions      Interactive IGV visualisation (Shiny +
                        igvShiny) of differential regions
calculate_and_add_occupancy_pvals
                        Calculate and add gene occupancy FDR
calculate_occupancy     Compute occupancy for genomic regions
conditionNames          Access condition name mapping
differential_accessibility
                        Differential accessibility analysis for CATaDa
                        ('NOISeq' based)
differential_binding    Differential binding/expression analysis
                        ('limma')
enrichedCond1           Access Condition 1 enriched regions
enrichedCond2           Access Condition 2 enriched regions
expressed               Get expressed genes/loci by FDR
extract_unique_sample_ids
                        Extract unique sample names from complex labels
filter_genes_by_fdr     Filter genes by FDR within a specific condition
get_ensdb_genes         Extract gene annotation from Ensembl via
                        AnnotationHub EnsDb
inputData               Access original input data and metadata
load_data_genes         Load genome-wide binding data for gene
                        expression (RNA polymerase occupancy)
load_data_peaks         Load genome-wide binding data and associated
                        peak files or GRanges objects
plot_input_diagnostics
                        Display diagnostic plots for input data
plot_limma_diagnostics
                        Verify Underlying Assumptions for 'limma'
                        Analysis
plot_venn               Draw proportional Venn diagrams for
                        differential binding analysis
plot_volcano            Volcano plot of differentially bound/expressed
                        loci
quantile_normalisation
                        Quantile normalisation (native R code version)
reduce_regions          Reduce a list of GRanges to unique,
                        non-overlapping regions
sample_labels_by_isolation
                        Sample data points based on local isolation
