BaitCapture             Bait capture efficiency
BinMethylation          Summarize methylation inside sorting bins
CallContextMethylation
                        Call Context Methylation
CollapseStrands         Collapse strands
CollapseStrandsSM       Collapse strands in single molecule matrix
ConversionRate          Conversion rate
CoverageFilter          Filter Cs for coverage
DetectExperimentType    Detect type of experiment
FilterByConversionRate
                        Calculate reads conversion rate
FilterContextCytosines
                        Filter Cytosines in context
FixOverhang             Fixing overhang before stand collapsing
GetQuasRprj             Get QuasRprj
GetSingleMolMethMat     Get Single Molecule methylation matrix
HierarchicalClustering
                        Perform Hierarchical clustering on single reads
OneTFstates             Design states for single TF case
PlotAvgSMF              Plot average methylation
PlotSM                  Wrapper for PlotSingleMoleculeStack function
PlotSingleMoleculeStack
                        Plot single molecule stack
PlotSingleSiteSMF       Plot SMF data at single site
SampleCorrelation       Intersample correlation
SingleTFStateQuantificationPlot
                        Single TF state quantification bar
SortReads               Sort reads by single TF
SortReadsBySingleTF     Wrapper to SortReads for single TF case
SortReadsByTFCluster    Wrapper to SortReads for TF cluster case
StateQuantificationPlot
                        Plot states quantification bar
TFPairStateQuantificationPlot
                        TF pair state quantification bar
TFpairStates            Design states for TF pair case
