appendCeldaList	appendCeldaList
availableModels	availableModels
bestLogLikelihood	bestLogLikelihood
bestLogLikelihood,celdaModel-method	bestLogLikelihood
bestLogLikelihood,SingleCellExperiment-method	bestLogLikelihood
celda	celda
celdaCGGridSearchRes	celdaCGGridSearchRes
celdaCGMod	celdaCGMod
celdaCGSim	celdaCGSim
celdaClusters	celdaClusters
celdaClusters,celdaModel-method	celdaClusters
celdaClusters,SingleCellExperiment-method	celdaClusters
celdaClusters<-	celdaClusters
celdaClusters<-,SingleCellExperiment-method	celdaClusters
celdaCMod	celdaCMod
celdaCSim	celdaCSim
celdaGMod	celdaGMod
celdaGridSearch	celdaGridSearch
celdaGridSearch,matrix-method	celdaGridSearch
celdaGridSearch,SingleCellExperiment-method	celdaGridSearch
celdaGSim	celdaGSim
celdaHeatmap	celdaHeatmap
celdaHeatmap,SingleCellExperiment-method	celdaHeatmap
celdaModel	celdaModel
celdaModel,SingleCellExperiment-method	celdaModel
celdaModules	celdaModules
celdaModules,SingleCellExperiment-method	celdaModules
celdaModules<-	celdaModules
celdaModules<-,SingleCellExperiment-method	celdaModules
celdaPerplexity	celdaPerplexity
celdaPerplexity,celdaList-method	celdaPerplexity-celdaList-method
celdaProbabilityMap	celdaProbabilityMap
celdaProbabilityMap,SingleCellExperiment-method	celdaProbabilityMap
celdatosce	celdatosce
celdatosce,celdaList-method	celdatosce
celdatosce,celda_C-method	celdatosce
celdatosce,celda_CG-method	celdatosce
celdatosce,celda_G-method	celdatosce
celdaTsne	celdaTsne
celdaTsne,SingleCellExperiment-method	celdaTsne
celdaUmap	celdaUmap
celdaUmap,SingleCellExperiment-method	celdaUmap
celda_C	celda_C
celda_C,ANY-method	celda_C
celda_C,SingleCellExperiment-method	celda_C
celda_CG	celda_CG
celda_CG,ANY-method	celda_CG
celda_CG,SingleCellExperiment-method	celda_CG
celda_G	celda_G
celda_G,ANY-method	celda_G
celda_G,SingleCellExperiment-method	celda_G
clusterProbability	clusterProbability
clusterProbability,SingleCellExperiment-method	clusterProbability
compareCountMatrix	compareCountMatrix
compareCountMatrix,ANY,celdaList-method	compareCountMatrix
compareCountMatrix,ANY,celdaModel-method	compareCountMatrix
contaminationSim	contaminationSim
countChecksum	countChecksum
countChecksum,celdaList-method	countChecksum-celdaList-method
decontX	decontX
decontX,ANY-method	decontX
decontX,SingleCellExperiment-method	decontX
decontXcounts	decontXcounts
decontXcounts,SingleCellExperiment-method	decontXcounts
decontXcounts<-	decontXcounts
decontXcounts<-,SingleCellExperiment-method	decontXcounts
distinctColors	distinctColors
eigenMatMultInt	eigenMatMultInt
eigenMatMultNumeric	eigenMatMultNumeric
factorizeMatrix	factorizeMatrix
factorizeMatrix,ANY,celda_C-method	factorizeMatrix
factorizeMatrix,ANY,celda_CG-method	factorizeMatrix
factorizeMatrix,ANY,celda_G-method	factorizeMatrix
factorizeMatrix,SingleCellExperiment,ANY-method	factorizeMatrix
fastNormProp	fastNormProp
fastNormPropLog	fastNormPropLog
fastNormPropSqrt	fastNormPropSqrt
featureModuleLookup	featureModuleLookup
featureModuleLookup,SingleCellExperiment-method	featureModuleLookup
featureModuleTable	featureModuleTable
findMarkersTree	findMarkersTree
geneSetEnrich	geneSetEnrich
geneSetEnrich,matrix-method	geneSetEnrich
geneSetEnrich,SingleCellExperiment-method	geneSetEnrich
getDecisions	getDecisions
logLikelihood	logLikelihood
logLikelihood,matrix,celda_C-method	logLikelihood
logLikelihood,matrix,celda_CG-method	logLikelihood
logLikelihood,matrix,celda_G-method	logLikelihood
logLikelihood,SingleCellExperiment,ANY-method	logLikelihood
logLikelihoodHistory	logLikelihoodHistory
logLikelihoodHistory,celdaModel-method	logLikelihoodHistory
logLikelihoodHistory,SingleCellExperiment-method	logLikelihoodHistory
matrixNames	matrixNames
matrixNames,celdaModel-method	matrixNames
moduleHeatmap	moduleHeatmap
moduleHeatmap,SingleCellExperiment-method	moduleHeatmap
nonzero	nonzero
normalizeCounts	normalizeCounts
params	params
params,celdaModel-method	params
perplexity	perplexity
perplexity,ANY,celda_C-method	perplexity
perplexity,ANY,celda_CG-method	perplexity
perplexity,ANY,celda_G-method	perplexity
perplexity,SingleCellExperiment,ANY-method	perplexity
plotCeldaViolin	plotCeldaViolin
plotCeldaViolin,ANY-method	plotCeldaViolin
plotCeldaViolin,SingleCellExperiment-method	plotCeldaViolin
plotDecontXContamination	plotDecontXContamination
plotDecontXMarkerExpression	plotDecontXMarkerExpression
plotDecontXMarkerPercentage	plotDecontXMarkerPercentage
plotDendro	plotDendro
plotDimReduceCluster	plotDimReduceCluster
plotDimReduceCluster,SingleCellExperiment-method	plotDimReduceCluster
plotDimReduceCluster,vector-method	plotDimReduceCluster
plotDimReduceFeature	plotDimReduceFeature
plotDimReduceFeature,ANY-method	plotDimReduceFeature
plotDimReduceFeature,SingleCellExperiment-method	plotDimReduceFeature
plotDimReduceGrid	plotDimReduceGrid
plotDimReduceGrid,ANY-method	plotDimReduceGrid
plotDimReduceGrid,SingleCellExperiment-method	plotDimReduceGrid
plotDimReduceModule	plotDimReduceModule
plotDimReduceModule,ANY-method	plotDimReduceModule
plotDimReduceModule,SingleCellExperiment-method	plotDimReduceModule
plotGridSearchPerplexity	plotGridSearchPerplexity
plotGridSearchPerplexity,celdaList-method	plotGridSearchPerplexity
plotGridSearchPerplexity,SingleCellExperiment-method	plotGridSearchPerplexity
plotHeatmap	plotHeatmap
plotMarkerHeatmap	plotMarkerHeatmap
plotRPC	plotRPC
plotRPC,celdaList-method	plotRPC
plotRPC,SingleCellExperiment-method	plotRPC
recodeClusterY	recodeClusterY
recodeClusterZ	recodeClusterZ
recursiveSplitCell	recursiveSplitCell
recursiveSplitCell,matrix-method	recursiveSplitCell
recursiveSplitCell,SingleCellExperiment-method	recursiveSplitCell
recursiveSplitModule	recursiveSplitModule
recursiveSplitModule,matrix-method	recursiveSplitModule
recursiveSplitModule,SingleCellExperiment-method	recursiveSplitModule
reorderCelda	reorderCelda
reorderCelda,matrix,celda_C-method	reorderCelda
reorderCelda,matrix,celda_CG-method	reorderCelda
reorderCelda,matrix,celda_G-method	reorderCelda
reorderCelda,SingleCellExperiment,ANY-method	reorderCelda
reportceldaCG	reportceldaCG
reportCeldaCGPlotResults	reportceldaCG
reportCeldaCGRun	reportceldaCG
resamplePerplexity	resamplePerplexity
resamplePerplexity,ANY-method	resamplePerplexity
resamplePerplexity,SingleCellExperiment-method	resamplePerplexity
resList	resList
resList,celdaList-method	resList
resList,SingleCellExperiment-method	resList
retrieveFeatureIndex	retrieveFeatureIndex
runParams	runParams
runParams,celdaList-method	runParams
runParams,SingleCellExperiment-method	runParams
sampleCells	sampleCells
sampleLabel	sampleLabel
sampleLabel,celdaModel-method	sampleLabel
sampleLabel,SingleCellExperiment-method	sampleLabel
sampleLabel<-	sampleLabel
sampleLabel<-,SingleCellExperiment-method	sampleLabel
sceCeldaC	sceCeldaC
sceCeldaCG	sceCeldaCG
sceCeldaCGGridSearch	sceCeldaCGGridSearch
sceCeldaG	sceCeldaG
selectBestModel	selectBestModel
selectBestModel,celdaList-method	selectBestModel
selectBestModel,SingleCellExperiment-method	selectBestModel
selectFeatures	selectFeatures
selectFeatures,matrix-method	selectFeatures
selectFeatures,SingleCellExperiment-method	selectFeatures
semiPheatmap	semiPheatmap
simulateCells	simulateCells
simulateContamination	simulateContamination
splitModule	splitModule
splitModule,SingleCellExperiment-method	splitModule
subsetCeldaList	subsetCeldaList
subsetCeldaList,celdaList-method	subsetCeldaList
subsetCeldaList,SingleCellExperiment-method	subsetCeldaList
topRank	topRank
