buildAnnotationDatabase
                        Build a local annotation database for recoup
buildAnnotationStore    Build a local annotation database for recoup
buildCustomAnnotation   Import custom annotation to the recoup
                        annotation database from GTF file
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
getInstalledAnnotations
                        Load a recoup annotation element
getr                    Get and set some reusable objects from a recoup
                        object
importCustomAnnotation
                        Import a recoup custom annotation element
kmeansDesign            Apply k-means clustering to profile data
loadAnnotation          Load a recoup annotation element
mergeRuns               Merge recoup outputs of same type
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
recoup-defunct          Defunct functions in package 'recoup'
recoup-deprecated       Deprecated functions in package 'recoup'
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
rpMatrix                Reads per million profile matrices for plotting
sliceObj                Subset recoup output list objects
