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| 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 |
| PlotSingleMoleculeStack | Plot single molecule stack |
| PlotSingleSiteSMF | Plot SMF data at single site |
| PlotSM | Wrapper for PlotSingleMoleculeStack function |
| 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 |