.callOpenTiles_ArchR	callOpenTiles-methods
.counts_plot_default_theme	dot-counts_plot_default_theme
.gene_plot_theme	dot-gene_plot_theme
addAccessibilityShift	addAccessibilityShift
addMotifSet	addMotifSet
annotateTiles	annotateTiles
bulkDimReduction	bulkDimReduction
bulkUMAP	bulkUMAP
callOpenTiles	callOpenTiles-methods
callOpenTiles,ArchRProject-method	callOpenTiles-methods
callOpenTiles,GRangesList-method	callOpenTiles-methods
callOpenTiles,list-method	callOpenTiles-methods
combineSampleTileMatrix	combineSampleTileMatrix
differentialsToGRanges	differentialsToGRanges
exampleBlackList	exampleBlackList
exampleCellColData	exampleCellColData
exampleFragments	exampleFragments
extractErrorFromConsensusTiles	extractErrorFromConsensusTiles
extractRegion	extractRegion
filterCoAccessibleLinks	filterCoAccessibleLinks
finalModelObject	finalModelObject
getAltTSS	getAltTSS
getCellPopMatrix	getCellPopMatrix
getCoAccessibleLinks	getCoAccessibleLinks
getCoverage	getCoverage
getDifferentialAccessibleTiles	getDifferentialAccessibleTiles
getModelValues	getModelValues
getPopFrags	getPopFrags
getSampleTileMatrix	getSampleTileMatrix
GRangesToString	GRangesToString
MotifEnrichment	MotifEnrichment
MotifSetEnrichmentAnalysis	MotifSetEnrichmentAnalysis
pilotLMEM	pilotLMEM
pilotZIGLMM	pilotZIGLMM
plotConsensus	plotConsensus
plotRegion	plotRegion
runLMEM	runLMEM
runZIGLMM	runZIGLMM
simplifiedConsensusTiles	simplifiedConsensusTiles
singlePopulationConsensusTiles	singlePopulationConsensusTiles
singlePopulationSampleTileMatrix	singlePopulationSampleTileMatrix
StringsToGRanges	StringsToGRanges
subsetMOCHAObject	subsetMOCHAObject
testCoAccessibility	testCoAccessibility
testCoAccessibilityChromVar	testCoAccessibilityChromVar
testCoAccessibilityRandom	testCoAccessibilityRandom
youden_threshold	youden_threshold
