check_package           Check if a package is installed
forceReverse            Force reversal of a subset of the ordering
human_bm                Human gene symbols and positions
initialOrder            Ordering the molecules/reads
methyl_average_status   Calculate the average methylation/accessibility
                        status across all cells/molecules.
methyl_percent_sites    Calculates the percentage of methylated
                        cells/molecules per site
methyl_proportion       Calculate the proportion of methylated bases
                        for each cell/molecule
methylscaper            methylscaper
mouse_bm                Mouse gene symbols and positions
plotSequence            Generate Sequence Plot
prepSC                  Process single-cell data
reads_sm                Example reads from single-molecule experiment
ref_seq                 Example reference sequence to align reads to
                        from a single-molecule experiment
refineFunction          Refinement
reformatSCE             This is an internal function for now and a
                        place-holder in case SingleCellExperiment may
                        be used in the future. We may need to update
                        this later. Assumes rownames are formatted like
                        chr_pos and there are two assays. The assay
                        names are 'methylation_met' for endogenous
                        methylation and 'methylation_acc' for
                        accessibility.
runAlign                Align the single-molecule data
singlecell_subset       Example preprocessed single-cell experiment
                        subset
singlemolecule_example
                        Example preprocessed single-molecule experiment
subsetSC                Load in methylation data
