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
calculateGenesCE	GenesStatistics
calculateMu	CalculatingCOEX
calculateMu,COTAN-method	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	COTAN
COTAN-class	COTAN-class
COTANObjectCreation	COTANObjectCreation
Datasets	Datasets
datasetTags	HandleMetaData
DEAOnClusters	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	GenesCoexSpace
estimateDispersionBisection	ParametersEstimations
estimateDispersionBisection,COTAN-method	ParametersEstimations
estimateDispersionNuBisection	ParametersEstimations
estimateDispersionNuBisection,COTAN-method	ParametersEstimations
estimateDispersionNuNlminb,COTAN-method	ParametersEstimations
estimateLambdaLinear	ParametersEstimations
estimateLambdaLinear,COTAN-method	ParametersEstimations
estimateNuBisection,COTAN-method	ParametersEstimations
estimateNuLinear	ParametersEstimations
estimateNuLinear,COTAN-method	ParametersEstimations
estimateNuLinearByCluster	HandlingClusterizations
estimateNuLinearByCluster,COTAN-method	HandlingClusterizations
expectedContingencyTables	CalculatingCOEX
expectedContingencyTablesNN	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	funProbZero
GDIPlot	UniformClusters
GenesCoexSpace	GenesCoexSpace
genesCoexSpace	GenesCoexSpace
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
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
getNormalizedData,COTAN-method	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
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
LegacyFastSymmMatrix	LegacyFastSymmMatrix
LoggingFunctions	LoggingFunctions
logThis	LoggingFunctions
mat2vec_rfast	LegacyFastSymmMatrix
mergeClusters	ClustersList
mergeUniformCellsClusters	UniformClusters
mitochondrialPercentagePlot	RawDataCleaning
multiMergeClusters	ClustersList
normalizeNameAndLabels	HandlingConditions
observedContingencyTables	CalculatingCOEX
observedContingencyTablesYY	CalculatingCOEX
ParametersEstimations	ParametersEstimations
plotTheme	HeatmapPlots
proceedToCoex	COTANObjectCreation
proceedToCoex,COTAN-method	COTANObjectCreation
pValueFromDEA	HandlingClusterizations
raw.dataset	Datasets
RawDataCleaning	RawDataCleaning
RawDataGetters	RawDataGetters
reorderClusterization	HandlingClusterizations
scatterPlot	RawDataCleaning
scCOTAN	scCOTAN
scCOTAN-class	scCOTAN
setColumnInDF	HandleMetaData
setLoggingFile	LoggingFunctions
setLoggingLevel	LoggingFunctions
test.dataset	Datasets
test.dataset.clusters1	Datasets
test.dataset.clusters2	Datasets
toClustersList	ClustersList
UMAPPlot	HandlingClusterizations
UniformClusters	UniformClusters
vec2mat_rfast	LegacyFastSymmMatrix
