.detect.footprints	dot-detect.footprints
AggregateFootprints	AggregateFootprints
AnnotateFootprints	AnnotateFootprints
Arrange_TFBSs_clusters	Arrange_TFBSs_clusters
BaitCapture	BaitCapture
BinMethylation	BinMethylation
CallContextMethylation	CallContextMethylation
cbind_fill_sparseMatrix	cbind_fill_sparseMatrix
CollapseStrands	CollapseStrands
CollapseStrandsSM	CollapseStrandsSM
CollectCompositeData	CollectCompositeData
colMeans_drop0	colMeans_drop0
CompositeMethylationCorrelation	CompositeMethylationCorrelation
CompositePlot	CompositePlot
ConversionRate	ConversionRate
CoverageFilter	CoverageFilter
Create_MethylationCallingWindows	Create_MethylationCallingWindows
DetectExperimentType	DetectExperimentType
DetectFootprints	DetectFootprints
fill.empty.columns	fill.empty.columns
filter.dense.matrix	filter.dense.matrix
FilterByConversionRate	FilterByConversionRate
FilterContextCytosines	FilterContextCytosines
filter_reads_from_MethGR	filter_reads_from_MethGR
FootprintCharter	FootprintCharter
full.join.granges	full.join.granges
GetQuasRprj	GetQuasRprj
GetSingleMolMethMat	GetSingleMolMethMat
GRanges_to_DF	GRanges_to_DF
HierarchicalClustering	HierarchicalClustering
LowCoverageMethRate_RMSE	LowCoverageMethRate_RMSE
MaskSNPs	MaskSNPs
matrix.sliding.window.average	matrix.sliding.window.average
MethSM.to.dense	MethSM.to.dense
MethSM.to.MethGR	MethSM.to.MethGR
panel.cor	panel.cor
panel.hist	panel.hist
panel.jet	panel.jet
PlotAvgSMF	PlotAvgSMF
PlotFootprints	PlotFootprints
PlotSingleMoleculeStack	PlotSingleMoleculeStack
PlotSingleSiteSMF	PlotSingleSiteSMF
PlotSM	PlotSM
Plot_FootprintCharter_SM	Plot_FootprintCharter_SM
Plot_LowCoverageMethRate	Plot_LowCoverageMethRate
Plot_LowCoverageMethRate_RMSE	Plot_LowCoverageMethRate_RMSE
rbind_fill_sparseMatrix	rbind_fill_sparseMatrix
RollingMean	RollingMean
rowMeans_drop0	rowMeans_drop0
SingleTFStateQuantificationPlot	SingleTFStateQuantificationPlot
SingleTFStates	SingleTFStates
SortReads	SortReads
SortReadsBySingleTF	SortReadsBySingleTF
SortReadsBySingleTF_MultiSiteWrapper	SortReadsBySingleTF_MultiSiteWrapper
SortReadsByTFCluster	SortReadsByTFCluster
SortReadsByTFCluster_MultiSiteWrapper	SortReadsByTFCluster_MultiSiteWrapper
StateQuantification	StateQuantification
StateQuantificationBySingleTF	StateQuantificationBySingleTF
StateQuantificationByTFPair	StateQuantificationByTFPair
StateQuantificationPlot	StateQuantificationPlot
SubsetGRangesForSamples	SubsetGRangesForSamples
TFPairStateQuantificationPlot	TFPairStateQuantificationPlot
TFPairStates	TFPairStates
