bsConversionPlot        Bisulfite conversion rate visualization
chromosomeCoverage      CpG covergae in each chromosome
coverage                Coverage for single cells
cpgDensity              Provides Coverage by the CpG density. CpG
                        Density is defined as the number of CpGs
                        observed in certain base pair long region.
cpgDiscretization       Discretize the CpG methylation values to align
                        with single cell analysis
downsample              Downsample analysis
featureCoverage         Coverage based on the genomic feature
mbiasplot               Methylation bias plot
methylationDist         Provide graphics for methylation distribution
readmetrics             Provide graphics for read information
repMask                 Provides Coverage metrics in the repeat masker
                        region
report                  Generates an inclusive report on methylation
                        analysis
scmeth                  scmeth: a package to conduct quality control
                        analysis for methylation data. Most functions
                        can be applied to both bulk and single-cell
                        methylation while other functions are specific
                        to single-cell methylation data. scmeth is
                        especially customized to use the output from
                        the FireCloud implementation of methylation
                        pipeline to produce comprehensive quality
                        control report
