addClusterization	HandlingClusterizations
addClusterization,COTAN-method	HandlingClusterizations
addClusterizationCoex	HandlingClusterizations
addClusterizationCoex,COTAN-method	HandlingClusterizations
addCondition	HandlingConditions
addCondition,COTAN-method	HandlingConditions
addElementToMetaDataset	HandleMetaData
addElementToMetaDataset,COTAN-method	HandleMetaData
AdvancedGDIUniformityCheck-class	UniformTranscriptCheckers
asClusterization	ClustersList
automaticCOTANObjectCreation	COTAN_ObjectCreation
BaseUniformityCheck-class	UniformTranscriptCheckers
calcDist	NumericUtilities
calculateCoex	CalculatingCOEX
calculateCoex,COTAN-method	CalculatingCOEX
calculateG	CalculatingCOEX
calculateGDI	GenesStatistics
calculateGDIGivenCorr	GenesStatistics
calculateGDIGivenS	GenesStatistics
calculateGenesCE	GenesStatistics
calculateLikelihoodOfObserved	CalculatingCOEX
calculateMu	CalculatingCOEX
calculatePartialCoex	CalculatingCOEX
calculatePDI	GenesStatistics
calculatePValue	GenesStatistics
calculateReducedDataMatrix	CalculatingCOEX
calculateS	CalculatingCOEX
calculateThresholdShiftToUniformity	UniformTranscriptCheckers
calculateThresholdShiftToUniformity,AdvancedGDIUniformityCheck-method	UniformTranscriptCheckers
calculateThresholdShiftToUniformity,SimpleGDIUniformityCheck-method	UniformTranscriptCheckers
CalculatingCOEX	CalculatingCOEX
canUseTorch	MultiThreading
cellsHeatmapPlot	HeatmapPlots
cellSizePlot	RawDataCleaning
cellsUMAPPlot	HandlingClusterizations
cellsUniformClustering	UniformClusters
checkClusterUniformity	UniformClusters
checkersToDF	UniformTranscriptCheckers
checkObjIsUniform	UniformTranscriptCheckers
checkObjIsUniform,AdvancedGDIUniformityCheck-method	UniformTranscriptCheckers
checkObjIsUniform,SimpleGDIUniformityCheck-method	UniformTranscriptCheckers
clean	RawDataCleaning
clean,COTAN-method	RawDataCleaning
cleanPlots	RawDataCleaning
clusterGeneContingencyTables	HandlingClusterizations
clustersDeltaExpression	COTAN_Legacy
ClustersList	ClustersList
clustersMarkersHeatmapPlot	HandlingClusterizations
clustersSummaryData	HandlingClusterizations
clustersSummaryPlot	HandlingClusterizations
clustersTreePlot	HandlingClusterizations
conditionsFromNames	HandleStrings
contingencyTables	CalculatingCOEX
Conversions	Conversions
convertFromSingleCellExperiment	Conversions
convertToSingleCellExperiment	Conversions
COTAN	COTAN_ObjectCreation
COTAN-class	COTAN-class
COTAN_coerce_to_scCOTAN	COTAN_Legacy
COTAN_Legacy	COTAN_Legacy
COTAN_ObjectCreation	COTAN_ObjectCreation
Datasets	Datasets
datasetTags	HandleMetaData
DEAOnClusters	HandlingClusterizations
dfToCheckers	UniformTranscriptCheckers
dispersionBisection	NumericUtilities
dispersionNewton	NumericUtilities
distancesBetweenClusters	HandlingClusterizations
dropCellsCoex	CalculatingCOEX
dropCellsCoex,COTAN-method	CalculatingCOEX
dropClusterization	HandlingClusterizations
dropClusterization,COTAN-method	HandlingClusterizations
dropCondition	HandlingConditions
dropCondition,COTAN-method	HandlingConditions
dropGenesCells	RawDataCleaning
dropGenesCells,COTAN-method	RawDataCleaning
dropGenesCoex	CalculatingCOEX
dropGenesCoex,COTAN-method	CalculatingCOEX
ECDPlot	RawDataCleaning
ERCCraw	Datasets
establishGenesClusters	GenesStatistics
estimateDispersionBisection	ParametersEstimations
estimateDispersionNuBisection	ParametersEstimations
estimateDispersionNuBisection,COTAN-method	ParametersEstimations
estimateDispersionNuNlminb	ParametersEstimations
estimateDispersionNuNlminb,COTAN-method	ParametersEstimations
estimateDispersionViaSolver	ParametersEstimations
estimateDispersionViaSolver,COTAN-method	ParametersEstimations
estimateLambdaLinear	ParametersEstimations
estimateLambdaLinear,COTAN-method	ParametersEstimations
estimateNuBisection	ParametersEstimations
estimateNuBisection,COTAN-method	ParametersEstimations
estimateNuLinear	ParametersEstimations
estimateNuLinear,COTAN-method	ParametersEstimations
estimateNuLinearByCluster	HandlingClusterizations
estimateNuLinearByCluster,COTAN-method	HandlingClusterizations
estimatorsAreReady	ParametersEstimations
expectedContingencyTables	CalculatingCOEX
expectedContingencyTablesNN	CalculatingCOEX
expectedPartialContingencyTables	CalculatingCOEX
expectedPartialContingencyTablesNN	CalculatingCOEX
factorToVector	HandleStrings
findClustersMarkers	HandlingClusterizations
findFullyExpressedGenes	RawDataCleaning
findFullyExpressedGenes,COTAN-method	RawDataCleaning
findFullyExpressingCells	RawDataCleaning
findFullyExpressingCells,COTAN-method	RawDataCleaning
flagNotFullyExpressedGenes	RawDataCleaning
flagNotFullyExpressedGenes,COTAN-method	RawDataCleaning
flagNotFullyExpressingCells	RawDataCleaning
flagNotFullyExpressingCells,COTAN-method	RawDataCleaning
fromClustersList	ClustersList
funProbZero	NumericUtilities
GDICheck-class	UniformTranscriptCheckers
GDIPlot	UniformClusters
genesCoexSpace	GenesStatistics
geneSetEnrichment	HandlingClusterizations
genesHeatmapPlot	HeatmapPlots
genesPercentagePlot	RawDataCleaning
genesSizePlot	RawDataCleaning
GenesStatistics	GenesStatistics
getAllConditions	HandlingConditions
getAllConditions,COTAN-method	HandlingConditions
getCells	RawDataGetters
getCells,COTAN-method	RawDataGetters
getCellsCoex	CalculatingCOEX
getCellsCoex,COTAN-method	CalculatingCOEX
getCellsSize	RawDataGetters
getCellsSize,COTAN-method	RawDataGetters
getCheckerThreshold	UniformTranscriptCheckers
getCheckerThreshold,AdvancedGDIUniformityCheck-method	UniformTranscriptCheckers
getCheckerThreshold,SimpleGDIUniformityCheck-method	UniformTranscriptCheckers
getClusterizationData	HandlingClusterizations
getClusterizationData,COTAN-method	HandlingClusterizations
getClusterizationName	HandlingClusterizations
getClusterizationName,COTAN-method	HandlingClusterizations
getClusterizations	HandlingClusterizations
getClusterizations,COTAN-method	HandlingClusterizations
getClusters	HandlingClusterizations
getClustersCoex	HandlingClusterizations
getClustersCoex,COTAN-method	HandlingClusterizations
getColorsVector	getColorsVector
getColumnFromDF	HandleMetaData
getCondition	HandlingConditions
getCondition,COTAN-method	HandlingConditions
getConditionName	HandlingConditions
getConditionName,COTAN-method	HandlingConditions
getDataMatrix	CalculatingCOEX
getDims	HandleMetaData
getDims,COTAN-method	HandleMetaData
getDispersion	ParametersEstimations
getDispersion,COTAN-method	ParametersEstimations
getFullyExpressedGenes	RawDataCleaning
getFullyExpressedGenes,COTAN-method	RawDataCleaning
getFullyExpressingCells	RawDataCleaning
getFullyExpressingCells,COTAN-method	RawDataCleaning
getGDI	GenesStatistics
getGDI,COTAN-method	GenesStatistics
getGenes	RawDataGetters
getGenes,COTAN-method	RawDataGetters
getGenesCoex	CalculatingCOEX
getGenesCoex,COTAN-method	CalculatingCOEX
getGenesSize	RawDataGetters
getGenesSize,COTAN-method	RawDataGetters
getLambda	ParametersEstimations
getLambda,COTAN-method	ParametersEstimations
getLogNormData	ParametersEstimations
getMetadataCells	HandleMetaData
getMetadataCells,COTAN-method	HandleMetaData
getMetadataDataset	HandleMetaData
getMetadataDataset,COTAN-method	HandleMetaData
getMetadataElement	HandleMetaData
getMetadataElement,COTAN-method	HandleMetaData
getMetadataGenes	HandleMetaData
getMetadataGenes,COTAN-method	HandleMetaData
getMetaInfoRow	HandleMetaData
getMu	CalculatingCOEX
getNormalizedData	ParametersEstimations
getNu	ParametersEstimations
getNu,COTAN-method	ParametersEstimations
getNumCells	RawDataGetters
getNumCells,COTAN-method	RawDataGetters
getNumExpressedGenes	RawDataGetters
getNumExpressedGenes,COTAN-method	RawDataGetters
getNumGenes	RawDataGetters
getNumGenes,COTAN-method	RawDataGetters
getNumOfExpressingCells	RawDataGetters
getNumOfExpressingCells,COTAN-method	RawDataGetters
getNuNormData	ParametersEstimations
getProbabilityOfZero	ParametersEstimations
getRawData	RawDataGetters
getRawData,COTAN-method	RawDataGetters
getSelectedGenes	CalculatingCOEX
getZeroOneProj	RawDataGetters
getZeroOneProj,COTAN-method	RawDataGetters
groupByClusters	ClustersList
groupByClustersList	ClustersList
HandleMetaData	HandleMetaData
handleMultiCore	MultiThreading
handleNamesSubsets	HandleStrings
HandleStrings	HandleStrings
HandlingClusterizations	HandlingClusterizations
HandlingConditions	HandlingConditions
heatmapPlot	HeatmapPlots
HeatmapPlots	HeatmapPlots
initializeMetaDataset	HandleMetaData
initializeMetaDataset,COTAN-method	HandleMetaData
Installing_torch	Installing_torch
isCoexAvailable	CalculatingCOEX
isCoexAvailable,COTAN-method	CalculatingCOEX
isEmptyName	HandleStrings
logFoldChangeOnClusters	HandlingClusterizations
LoggingFunctions	LoggingFunctions
logThis	LoggingFunctions
mat2vec_rfast	COTAN_Legacy
mergeClusters	ClustersList
mergeUniformCellsClusters	UniformClusters
mitochondrialPercentagePlot	RawDataCleaning
multiMergeClusters	ClustersList
MultiThreading	MultiThreading
niceFactorLevels	HandleStrings
normalizeNameAndLabels	HandlingConditions
nuBisection	NumericUtilities
NumericUtilities	NumericUtilities
observedContingencyTables	CalculatingCOEX
observedContingencyTablesYY	CalculatingCOEX
observedPartialContingencyTables	CalculatingCOEX
observedPartialContingencyTablesYY	CalculatingCOEX
parallelDispersionBisection	NumericUtilities
parallelDispersionNewton	NumericUtilities
parallelNuBisection	NumericUtilities
ParametersEstimations	ParametersEstimations
plotTheme	HeatmapPlots
proceedToCoex	COTAN_ObjectCreation
proceedToCoex,COTAN-method	COTAN_ObjectCreation
pValueFromDEA	HandlingClusterizations
raw.dataset	Datasets
RawDataCleaning	RawDataCleaning
RawDataGetters	RawDataGetters
reorderClusterization	HandlingClusterizations
scatterPlot	RawDataCleaning
scCOTAN-class	COTAN_Legacy
scCotan_coerce_to_COTAN	COTAN_Legacy
screePlot	RawDataCleaning
setColumnInDF	HandleMetaData
setDispersion	RawDataCleaning
setDispersion,COTAN-method	RawDataCleaning
setLambda	RawDataCleaning
setLambda,COTAN-method	RawDataCleaning
setLoggingFile	LoggingFunctions
setLoggingLevel	LoggingFunctions
setNu	RawDataCleaning
setNu,COTAN-method	RawDataCleaning
shiftCheckerThresholds	UniformTranscriptCheckers
shiftCheckerThresholds,AdvancedGDIUniformityCheck,numeric-method	UniformTranscriptCheckers
shiftCheckerThresholds,SimpleGDIUniformityCheck,numeric-method	UniformTranscriptCheckers
SimpleGDIUniformityCheck-class	UniformTranscriptCheckers
singleHeatmapDF	HeatmapPlots
storeGDI	GenesStatistics
storeGDI,COTAN-method	GenesStatistics
test.dataset	Datasets
test.dataset.clusters1	Datasets
test.dataset.clusters2	Datasets
toClustersList	ClustersList
UMAPPlot	HandlingClusterizations
UniformClusters	UniformClusters
UniformTranscriptCheckers	UniformTranscriptCheckers
updateMetaInfo	HandleMetaData
vec2mat_rfast	COTAN_Legacy
vignette.cells.origin	Datasets
vignette.merge.clusters	Datasets
vignette.split.clusters	Datasets
