.counts_plot_default_theme
                        Default ggplot theme for counts plot
.gene_plot_theme        Common theme for gene plots
GRangesToString         'GRangesToString' Converts a GRanges object to
                        a string in the format 'chr1:100-200'
MotifEnrichment         'MotifEnrichment'
MotifSetEnrichmentAnalysis
                        'MotifSetEnrichmentAnalysis'
StringsToGRanges        'StringsToGRanges'
addAccessibilityShift   'addAccessibilityShift'
addMotifSet             'addMotifSet'
annotateTiles           'annotateTiles'
bulkDimReduction        'bulkDimReduction'
bulkUMAP                'bulkUMAP'
callOpenTiles           'callOpenTiles' Perform peak-calling on a set
                        of fragments or an ArchR Project.
combineSampleTileMatrix
                        'combineSampleTileMatrix'
differentialsToGRanges
                        'differentialsToGRanges' Converts a data.frame
                        matrix to a GRanges, preserving additional
                        columns as GRanges metadata
exampleBlackList        exampleBlackList
exampleCellColData      exampleCellColData
exampleFragments        exampleFragments
exportCoverage          'exportCoverage'
exportDifferentials     'exportDifferentials'
exportMotifs            'exportMotifs'
exportOpenTiles         'exportOpenTiles'
exportSmoothedInsertions
                        'exportSmoothedInsertions'
extractRegion           'extractRegion'
filterCoAccessibleLinks
                        'filterCoAccessibleLinks'
finalModelObject        finalModelObject
getAltTSS               Annotate Peaks falling in Transcription Start
                        Sites (TSS) and identify alternatively
                        regulated TSSs for each gene.
getAnnotationDbFromInstalledPkgname
                        'getAnnotationDbFromInstalledPkgname' Loads and
                        attaches an installed TxDb or OrgDb-class
                        Annotation database package.
getCellPopMatrix        'getCellPopMatrix'
getCellTypeTiles        'getCellTypeTiles' Extract the GRanges for a
                        particular cell type
getCellTypes            'getCellTypes' Extract cell type names from a
                        Tile Results or Sample Tile object.
getCoAccessibleLinks    'getCoAccessibleLinks'
getCoverage             Get sample-specific coverage files for each
                        sample-cell population.
getDifferentialAccessibleTiles
                        'getDifferentialAccessibleTiles'
getIntensityThreshold   'getIntensityThreshold'
getModelValues          getModelValues from runZIGLMM output.
getPopFrags             Extract fragments by populations from an ArchR
                        Project
getPromoterGenes        'getPromoterGenes'
getSampleCellTypeMetadata
                        'getSampleCellTypeMetadata' Extract
                        Sample-celltype specific metadata
getSampleTileMatrix     'getSampleTileMatrix'
getSequencingBias       'getSequencingBias'
mergeTileResults        'mergeTileResults'
packMOCHA               'packMOCHA'
pilotLMEM               Execute a pilot run of single linear model on a
                        subset of data
pilotZIGLMM             Execute a pilot run of model on a subset of
                        data
plotConsensus           'plotConsensus'
plotIntensityDistribution
                        'plotIntensityDistribution'
plotRegion              'plotRegion'
renameCellTypes         'renameCellTypes'
runLMEM                 Run Linear Mixed-Effects Modeling for
                        continuous, non-zero inflated data
runZIGLMM               Run Zero-inflated Generalized Linear Mixed
                        Modeling on pseudobulked scATAC data
subsetMOCHAObject       'subsetMOCHAObject'
testCoAccessibility     'testCoAccessibility'
unpackMOCHA             'unpackMOCHA'
varZIGLMM               Zero-inflated Variance Decomposition for
                        pseudobulked scATAC data
youden_threshold        youden_threshold
