addClusterization	HandlingClusterizations
addClusterization,COTAN-method	HandlingClusterizations
addClusterizationCoex	HandlingClusterizations
addClusterizationCoex,COTAN-method	HandlingClusterizations
addCondition	HandlingConditions
addCondition,COTAN-method	HandlingConditions
addElementToMetaDataset	HandleMetaData
addElementToMetaDataset,COTAN-method	HandleMetaData
automaticCOTANObjectCreation	COTANObjectCreation
calculateCoex	CalculatingCOEX
calculateCoex,COTAN-method	CalculatingCOEX
calculateG	CalculatingCOEX
calculateGDI	GenesStatistics
calculateGDIGivenCorr	GenesStatistics
calculateGenesCE	GenesStatistics
calculateMu	CalculatingCOEX
calculateMu,COTAN-method	CalculatingCOEX
calculatePartialCoex	CalculatingCOEX
calculatePDI	GenesStatistics
calculatePValue	GenesStatistics
calculateS	CalculatingCOEX
CalculatingCOEX	CalculatingCOEX
cellsHeatmapPlot	HeatmapPlots
cellSizePlot	RawDataCleaning
cellsUniformClustering	UniformClusters
checkClusterUniformity	UniformClusters
clean	RawDataCleaning
clean,COTAN-method	RawDataCleaning
cleanPlots	RawDataCleaning
clustersDeltaExpression	HandlingClusterizations
ClustersList	ClustersList
clustersMarkersHeatmapPlot	HandlingClusterizations
clustersSummaryData	HandlingClusterizations
clustersSummaryPlot	HandlingClusterizations
clustersTreePlot	HandlingClusterizations
contingencyTables	CalculatingCOEX
COTAN	COTANObjectCreation
COTAN-class	COTAN-class
COTAN-Legacy	COTAN-Legacy
COTANObjectCreation	COTANObjectCreation
Datasets	Datasets
datasetTags	HandleMetaData
DEAOnClusters	HandlingClusterizations
dispersionBisection	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
estimateDispersionBisection,COTAN-method	ParametersEstimations
estimateDispersionNuBisection	ParametersEstimations
estimateDispersionNuBisection,COTAN-method	ParametersEstimations
estimateDispersionNuNlminb	ParametersEstimations
estimateDispersionNuNlminb,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
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
GDIPlot	UniformClusters
genesCoexSpace	GenesStatistics
geneSetEnrichment	HandlingClusterizations
genesHeatmapPlot	HeatmapPlots
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
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
getCondition	HandlingConditions
getCondition,COTAN-method	HandlingConditions
getConditionName	HandlingConditions
getConditionName,COTAN-method	HandlingConditions
getDims	HandleMetaData
getDims,COTAN-method	HandleMetaData
getDispersion	ParametersEstimations
getDispersion,COTAN-method	ParametersEstimations
getFullyExpressedGenes	RawDataCleaning
getFullyExpressedGenes,COTAN-method	RawDataCleaning
getFullyExpressingCells	RawDataCleaning
getFullyExpressingCells,COTAN-method	RawDataCleaning
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
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
getRawData	RawDataGetters
getRawData,COTAN-method	RawDataGetters
getZeroOneProj	RawDataGetters
getZeroOneProj,COTAN-method	RawDataGetters
groupByClusters	ClustersList
groupByClustersList	ClustersList
HandleMetaData	HandleMetaData
HandlingClusterizations	HandlingClusterizations
HandlingConditions	HandlingConditions
heatmapPlot	HeatmapPlots
HeatmapPlots	HeatmapPlots
initializeMetaDataset	HandleMetaData
initializeMetaDataset,COTAN-method	HandleMetaData
Installing_torch	Installing_torch
isCoexAvailable	CalculatingCOEX
isCoexAvailable,COTAN-method	CalculatingCOEX
logFoldChangeOnClusters	HandlingClusterizations
LoggingFunctions	LoggingFunctions
logThis	LoggingFunctions
mat2vec_rfast	COTAN-Legacy
mergeClusters	ClustersList
mergeUniformCellsClusters	UniformClusters
mitochondrialPercentagePlot	RawDataCleaning
multiMergeClusters	ClustersList
normalizeNameAndLabels	HandlingConditions
nuBisection	NumericUtilities
NumericUtilities	NumericUtilities
observedContingencyTables	CalculatingCOEX
observedContingencyTablesYY	CalculatingCOEX
observedPartialContingencyTables	CalculatingCOEX
observedPartialContingencyTablesYY	CalculatingCOEX
parallelDispersionBisection	NumericUtilities
parallelNuBisection	NumericUtilities
ParametersEstimations	ParametersEstimations
plotTheme	HeatmapPlots
proceedToCoex	COTANObjectCreation
proceedToCoex,COTAN-method	COTANObjectCreation
pValueFromDEA	HandlingClusterizations
raw.dataset	Datasets
RawDataCleaning	RawDataCleaning
RawDataGetters	RawDataGetters
reorderClusterization	HandlingClusterizations
scatterPlot	RawDataCleaning
scCOTAN	COTAN-Legacy
scCOTAN-class	COTAN-Legacy
setColumnInDF	HandleMetaData
setLoggingFile	LoggingFunctions
setLoggingLevel	LoggingFunctions
singleHeatmapDF	HeatmapPlots
test.dataset	Datasets
test.dataset.clusters1	Datasets
test.dataset.clusters2	Datasets
toClustersList	ClustersList
UMAPPlot	HandlingClusterizations
UniformClusters	UniformClusters
vec2mat_rfast	COTAN-Legacy
vignette.merge.clusters	Datasets
vignette.split.clusters	Datasets
