TSSr-package	TSSr-package
annotateCluster	annotateCluster
annotateCluster,TSSr-method	annotateCluster
assignedClusters	TSSr-accessors
assignedClusters,TSSr-method	TSSr-accessors
callEnhancer	callEnhancer
callEnhancer,TSSr-method	callEnhancer
clusterShape	TSSr-accessors
clusterShape,TSSr-method	TSSr-accessors
clusterTSS	clusterTSS
clusterTSS,TSSr-method	clusterTSS
consensusCluster	consensusCluster
consensusCluster,TSSr-method	consensusCluster
consensusClusters	TSSr-accessors
consensusClusters,TSSr-method	TSSr-accessors
deGene	deGene
deGene,TSSr-method	deGene
DEtables	TSSr-accessors
DEtables,TSSr-method	TSSr-accessors
enhancers	TSSr-accessors
enhancers,TSSr-method	TSSr-accessors
exampleTSSr	exampleTSSr
exportClustersTable	exportClustersTable
exportClustersTable,TSSr-method	exportClustersTable
exportClustersToBed	exportClustersToBed
exportClustersToBed,TSSr-method	exportClustersToBed
exportDETable	exportDETable
exportDETable,TSSr-method	exportDETable
exportEnhancerTable	exportEnhancerTable
exportEnhancerTable,TSSr-method	exportEnhancerTable
exportShapeTable	exportShapeTable
exportShapeTable,TSSr-method	exportShapeTable
exportShiftTable	exportShiftTable
exportShiftTable,TSSr-method	exportShiftTable
exportTSStable	exportTSStable
exportTSStable,TSSr-method	exportTSStable
exportTSStoBedgraph	exportTSStoBedgraph
exportTSStoBedgraph,TSSr-method	exportTSStoBedgraph
filteredClusters	TSSr-accessors
filteredClusters,TSSr-method	TSSr-accessors
filterTSS	filterTSS
filterTSS,TSSr-method	filterTSS
getTSS	getTSS
getTSS,TSSr-method	getTSS
librarySizes	TSSr-accessors
librarySizes,TSSr-method	TSSr-accessors
mergeSamples	mergeSamples
mergeSamples,TSSr-method	mergeSamples
normalizeTSS	normalizeTSS
normalizeTSS,TSSr-method	normalizeTSS
plotCorrelation	plotCorrelation
plotCorrelation,TSSr-method	plotCorrelation
plotDE	plotDE
plotDE,TSSr-method	plotDE
plotInterQuantile	plotInterQuantile
plotInterQuantile,TSSr-method	plotInterQuantile
plotShape	plotShape
plotShape,TSSr-method	plotShape
plotTSS	plotTSS
plotTSS,TSSr-method	plotTSS
plotTssPCA	plotTssPCA
plotTssPCA,TSSr-method	plotTssPCA
PromoterShift	TSSr-accessors
PromoterShift,TSSr-method	TSSr-accessors
refTable	TSSr-accessors
refTable,TSSr-method	TSSr-accessors
shapeCluster	shapeCluster
shapeCluster,TSSr-method	shapeCluster
shiftPromoter	shiftPromoter
shiftPromoter,TSSr-method	shiftPromoter
show,TSSr-method	show-TSSr-method
tagClusters	TSSr-accessors
tagClusters,TSSr-method	TSSr-accessors
TAGtables	TSSr-accessors
TAGtables,TSSr-method	TSSr-accessors
TSSmatrix	TSSr-accessors
TSSmatrix,TSSr-method	TSSr-accessors
TSSr	TSSr-class
TSSr-accessors	TSSr-accessors
TSSr-class	TSSr-class
unassignedClusters	TSSr-accessors
unassignedClusters,TSSr-method	TSSr-accessors
