$.ArchRProject	cash-.ArchRProject
$<-.ArchRProject	cash-set-.ArchRProject
%bcin%	grapes-bcin-grapes
%bcni%	grapes-bcni-grapes
%ni%	grapes-ni-grapes
.DollarNames.ArchRProject	dot-DollarNames.ArchRProject
addArchRAnnotations	addArchRAnnotations
addArchRChrPrefix	addArchRChrPrefix
addArchRDebugging	addArchRDebugging
addArchRGenome	addArchRGenome
addArchRH5Level	addArchRH5Level
addArchRLocking	addArchRLocking
addArchRLogging	addArchRLogging
addArchRThreads	addArchRThreads
addArchRVerbose	addArchRVerbose
addBgdPeaks	addBgdPeaks
addCellColData	addCellColData
addClusters	addClusters
addCoAccessibility	addCoAccessibility
addCombinedDims	addCombinedDims
addDemuxletResults	addDemuxletResults
addDeviationsMatrix	addDeviationsMatrix
addDoubletScores	addDoubletScores
addFeatureCounts	addFeatureCounts
addFeatureMatrix	addFeatureMatrix
addGeneExpressionMatrix	addGeneExpressionMatrix
addGeneIntegrationMatrix	addGeneIntegrationMatrix
addGeneScoreMatrix	addGeneScoreMatrix
addGroupCoverages	addGroupCoverages
addHarmony	addHarmony
addImputeWeights	addImputeWeights
addIterativeLSI	addIterativeLSI
addModuleScore	addModuleScore
addMonocleTrajectory	addMonocleTrajectory
addMotifAnnotations	addMotifAnnotations
addPeak2GeneLinks	addPeak2GeneLinks
addPeakAnnotations	addPeakAnnotations
addPeakMatrix	addPeakMatrix
addPeakSet	addPeakSet
addProjectSummary	addProjectSummary
addReproduciblePeakSet	addReproduciblePeakSet
addSampleColData	addSampleColData
addSlingShotTrajectories	addSlingShotTrajectories
addTileMatrix	addTileMatrix
addTrajectory	addTrajectory
addTSNE	addTSNE
addUMAP	addUMAP
ArchRBrowser	ArchRBrowser
ArchRHeatmap	ArchRHeatmap
ArchRPalettes	ArchRPalettes
ArchRProject	ArchRProject
confusionMatrix	confusionMatrix
correlateMatrices	correlateMatrices
correlateTrajectories	correlateTrajectories
createArrowFiles	createArrowFiles
createGeneAnnotation	createGeneAnnotation
createGenomeAnnotation	createGenomeAnnotation
createLogFile	createLogFile
customEnrichment	customEnrichment
exportPeakMatrixForSTREAM	exportPeakMatrixForSTREAM
extendGR	extendGR
filterChrGR	filterChrGR
filterDoublets	filterDoublets
findMacs2	findMacs2
getArchRChrPrefix	getArchRChrPrefix
getArchRDebugging	getArchRDebugging
getArchRGenome	getArchRGenome
getArchRH5Level	getArchRH5Level
getArchRLogging	getArchRLogging
getArchRThreads	getArchRThreads
getArchRVerbose	getArchRVerbose
getArrowFiles	getArrowFiles
getAvailableMatrices	getAvailableMatrices
getBgdPeaks	getBgdPeaks
getBlacklist	getBlacklist
getCellColData	getCellColData
getCellNames	getCellNames
getChromLengths	getChromLengths
getChromSizes	getChromSizes
getCoAccessibility	getCoAccessibility
getEmbedding	getEmbedding
getExons	getExons
getFeatures	getFeatures
getFootprints	getFootprints
getFragmentsFromArrow	getFragmentsFromArrow
getFragmentsFromProject	getFragmentsFromProject
getGeneAnnotation	getGeneAnnotation
getGenes	getGenes
getGenome	getGenome
getGenomeAnnotation	getGenomeAnnotation
getGroupBW	getGroupBW
getGroupFragments	getGroupFragments
getGroupSE	getGroupSE
getGroupSummary	getGroupSummary
getImputeWeights	getImputeWeights
getInputFiles	getInputFiles
getMarkerFeatures	getMarkerFeatures
getMarkers	getMarkers
getMatches	getMatches
getMatrixFromArrow	getMatrixFromArrow
getMatrixFromProject	getMatrixFromProject
getMonocleTrajectories	getMonocleTrajectories
getOutputDirectory	getOutputDirectory
getPBGroupSE	getPBGroupSE
getPeak2GeneLinks	getPeak2GeneLinks
getPeakAnnotation	getPeakAnnotation
getPeakSet	getPeakSet
getPositions	getPositions
getProjectSummary	getProjectSummary
getReducedDims	getReducedDims
getSampleColData	getSampleColData
getSampleNames	getSampleNames
getSeqnames	getSeqnames
getTestArrow	getTestArrow
getTestFragments	getTestFragments
getTestProject	getTestProject
getTrajectory	getTrajectory
getTSS	getTSS
getTutorialData	getTutorialData
getValidBarcodes	getValidBarcodes
getVarDeviations	getVarDeviations
ggAlignPlots	ggAlignPlots
ggGroup	ggGroup
ggHex	ggHex
ggOneToOne	ggOneToOne
ggPoint	ggPoint
import10xFeatureMatrix	import10xFeatureMatrix
imputeMatrix	imputeMatrix
installExtraPackages	installExtraPackages
loadArchRProject	loadArchRProject
mapLabels	mapLabels
nCells	nCells
nonOverlappingGR	nonOverlappingGR
paletteContinuous	paletteContinuous
paletteDiscrete	paletteDiscrete
peakAnnoEnrichment	peakAnnoEnrichment
plotBrowserTrack	plotBrowserTrack
plotEmbedding	plotEmbedding
plotEnrichHeatmap	plotEnrichHeatmap
plotFootprints	plotFootprints
plotFragmentSizes	plotFragmentSizes
plotGroups	plotGroups
plotMarkerHeatmap	plotMarkerHeatmap
plotMarkers	plotMarkers
plotPDF	plotPDF
plotPeak2GeneHeatmap	plotPeak2GeneHeatmap
plotTrajectory	plotTrajectory
plotTrajectoryHeatmap	plotTrajectoryHeatmap
plotTSSEnrichment	plotTSSEnrichment
projectBulkATAC	projectBulkATAC
recoverArchRProject	recoverArchRProject
reformatFragmentFiles	reformatFragmentFiles
saveArchRProject	saveArchRProject
setArchRLocking	setArchRLocking
subsetArchRProject	subsetArchRProject
subsetCells	subsetCells
theme_ArchR	theme_ArchR
validBSgenome	validBSgenome
[.ArchRProject	sub-.ArchRProject
