DMRcaller               Call Differentially Methylated Regions (DMRs)
                        between two samples
DMRsNoiseFilterCG       The DMRs between WT and met1-3 in CG context
GEs                     The genetic elements data
GEs_hg38                The genetic elements data of GRCh38 Genome
                        Reference
PMDsBinsCG              The PMDs between GM18501 and GM18876 using Bins
                        method
PMDsNoiseFilterCG       The PMDs between GM18501 and GM18876 using
                        Noise_filter method
analyseReadsInsideRegionsForCondition
                        Analyse reads inside regions for condition
analyseReadsInsideRegionsForConditionPMD
                        Analyse reads inside regions for condition
computeCoMethylation    Compute pairwise co-methylation statistics for
                        cytosine sites within regions
computeDMRs             Compute DMRs
computeDMRsReplicates   Compute DMRs
computeMethylationDataCoverage
                        Compute methylation data coverage
computeMethylationDataSpatialCorrelation
                        Compute methylation data spatial correlation
computeMethylationProfile
                        Compute methylation profile
computeOverlapProfile   Compute Overlaps Profile
computePMDs             Compute PMDs
computeVMDs             Compute VMDs
extractGC               Extract GC
filterDMRs              Filter DMRs
filterPMDs              Filter PMDs
filterVMDs              Filter VMDs
filterVMRsONT           Filter VMRs for ONT Data
getWholeChromosomes     Get whole chromosomes from methylation data
joinReplicates          Joins together two GRange objects in a single
                        containing all the replicates
mergeDMRsIteratively    Merge DMRs iteratively
mergePMDsIteratively    Merge PMDs iteratively
methylationDataList     The methylation data list
ontSampleGRangesList    The ONT methylation data list
ont_gr_GM18870_chr1_PMD_bins_1k
                        Partially Methilated Domains example
ont_gr_GM18870_chr1_sorted_bins_1k
                        The ONT methylation data example
plotLocalMethylationProfile
                        Plot local methylation profile
plotMethylationDataCoverage
                        Plot methylation data coverage
plotMethylationDataSpatialCorrelation
                        Plot methylation data spatial correlation
plotMethylationProfile
                        Plot Methylation Profile
plotMethylationProfileFromData
                        Plot methylation profile from data
plotOverlapProfile      Plot overlap profile
poolMethylationDatasets
                        Pool methylation data
poolTwoMethylationDatasets
                        Pool two methylation datasets
readBismark             Read Bismark
readBismarkPool         Read Bismark pool
readONTbam              Load ONT BAM, decode MM/ML, and count modified
                        vs. unmodified reads
saveBismark             Save Bismark
scanBamChr1Random5      The bam file from ONT nanopore .pod5 files
selectCytosine          Select Cytosine Positions
syntheticDataReplicates
                        Simulated data for biological replicates
