buildAnnotationStore    Build a local annotation database for recoup
calcCoverage            Calculate coverages over a genomic region
coverageRef             Calculate coverage in a set of reference
                        genomic regions (ChIP-Seq or unspliced mode)
coverageRnaRef          Calculate coverage in a set of reference
                        genomic regions (RNA-Seq or spliced mode)
getAnnotation           Annotation downloader
getBiotypes             List default Ensembl biotypes
getr                    Get and set some reusable objects from a recoup
                        object
kmeansDesign            Apply k-means clustering to profile data
preprocessRanges        Read and preprocess BAM/BED files to GRanges
profileMatrix           Calculate final profile matrices for plotting
recoup                  Create genomic signal profiles in predefined or
                        custom areas using short sequence reads
recoupCorrelation       Plot (faceted) average genomic coverage
                        correlations
recoupHeatmap           Plot genomic coverage heatmaps
recoupPlot              Plot list objects returned by recoup
recoupProfile           Plot (faceted) average genomic coverage
                        profiles
recoup_test_data        Reference and genomic sample regions for recoup
                        testing
removeData              Remove data from recoup list object
sliceObj                Subset recoup output list objects
