API for seriph78/COTAN
COexpression Tables ANalysis

Global functions
AdvancedGDIUniformityCheck-class	Man page
BaseUniformityCheck-class	Man page
COTAN	Man page Source code
COTAN-class	Man page
COTAN_Legacy	Man page
COTAN_ObjectCreation	Man page
COTAN_coerce_to_scCOTAN	Man page
CalculatingCOEX	Man page
ClustersList	Man page
Conversions	Man page
DEAOnClusters	Man page Source code
Datasets	Man page
ECDPlot	Man page Source code
ERCCraw	Man page
GDICheck-class	Man page
GDIPlot	Man page Source code
GenesStatistics	Man page
HandleMetaData	Man page
HandleStrings	Man page
HandlingClusterizations	Man page
HandlingConditions	Man page
HeatmapPlots	Man page
Installing_torch	Man page
LoggingFunctions	Man page
MultiThreading	Man page
NumericUtilities	Man page
ParametersEstimations	Man page
RawDataCleaning	Man page
RawDataGetters	Man page
SimpleGDIUniformityCheck-class	Man page
UMAPPlot	Man page Source code
UniformClusters	Man page
UniformTranscriptCheckers	Man page
addClusterization	Man page
addClusterization,COTAN-method	Man page
addClusterizationCoex	Man page
addClusterizationCoex,COTAN-method	Man page
addCondition	Man page
addCondition,COTAN-method	Man page
addElementToMetaDataset	Man page
addElementToMetaDataset,COTAN-method	Man page
automaticCOTANObjectCreation	Man page Source code
calculateCoex	Man page
calculateCoex,COTAN-method	Man page
calculateCoex_Legacy	Source code
calculateG	Man page
calculateGDI	Man page Source code
calculateGDIGivenCorr	Man page Source code
calculateGDIGivenS	Source code
calculateGenesCE	Man page Source code
calculateLikelihoodOfObserved	Man page Source code
calculateMu	Man page
calculatePDI	Man page Source code
calculatePValue	Man page Source code
calculatePartialCoex	Man page
calculateS	Man page
calculateThresholdShiftToUniformity	Man page
calculateThresholdShiftToUniformity,AdvancedGDIUniformityCheck-m	Man page
calculateThresholdShiftToUniformity,SimpleGDIUniformityCheck-met	Man page
canUseTorch	Man page Source code
cellSizePlot	Man page Source code
cellsHeatmapPlot	Man page Source code
cellsUMAPPlot	Man page Source code
cellsUniformClustering	Man page Source code
checkClusterUniformity	Man page Source code
checkObjIsUniform	Man page
checkObjIsUniform,AdvancedGDIUniformityCheck-method	Man page
checkObjIsUniform,SimpleGDIUniformityCheck-method	Man page
checkersToDF	Man page Source code
clean	Man page
clean,COTAN-method	Man page
cleanPlots	Man page Source code
clustersDeltaExpression	Man page Source code
clustersMarkersHeatmapPlot	Man page Source code
clustersSummaryData	Man page Source code
clustersSummaryPlot	Man page Source code
clustersTreePlot	Man page Source code
conditionsFromNames	Man page Source code
contingencyTables	Man page Source code
convertFromSingleCellExperiment	Man page Source code
convertToSingleCellExperiment	Man page Source code
datasetTags	Man page Source code
dfToCheckers	Man page Source code
dispersionBisection	Man page Source code
distancesBetweenClusters	Man page Source code
dropCellsCoex	Man page
dropCellsCoex,COTAN-method	Man page
dropClusterization	Man page
dropClusterization,COTAN-method	Man page
dropCondition	Man page
dropCondition,COTAN-method	Man page
dropGenesCells	Man page
dropGenesCells,COTAN-method	Man page
dropGenesCoex	Man page
dropGenesCoex,COTAN-method	Man page
emptySparseMatrix	Source code
emptySymmetricMatrix	Source code
establishGenesClusters	Man page Source code
estimateDispersionBisection	Man page
estimateDispersionBisection,COTAN-method	Man page
estimateDispersionNuBisection	Man page
estimateDispersionNuBisection,COTAN-method	Man page
estimateDispersionNuNlminb	Man page
estimateDispersionNuNlminb,COTAN-method	Man page
estimateLambdaLinear	Man page
estimateLambdaLinear,COTAN-method	Man page
estimateNuBisection	Man page
estimateNuBisection,COTAN-method	Man page
estimateNuLinear	Man page
estimateNuLinear,COTAN-method	Man page
estimateNuLinearByCluster	Man page
estimateNuLinearByCluster,COTAN-method	Man page
estimatorsAreReady	Man page Source code
expectedContingencyTables	Man page Source code
expectedContingencyTablesNN	Man page Source code
expectedPartialContingencyTables	Man page Source code
expectedPartialContingencyTablesNN	Man page Source code
factorToVector	Man page Source code
findClustersMarkers	Man page Source code
findFullyExpressedGenes	Man page
findFullyExpressedGenes,COTAN-method	Man page
findFullyExpressingCells	Man page
findFullyExpressingCells,COTAN-method	Man page
flagNotFullyExpressedGenes	Man page
flagNotFullyExpressedGenes,COTAN-method	Man page
flagNotFullyExpressingCells	Man page
flagNotFullyExpressingCells,COTAN-method	Man page
fromClustersList	Man page Source code
funProbZero	Man page Source code
geneSetEnrichment	Man page Source code
genesCoexSpace	Man page Source code
genesHeatmapPlot	Man page Source code
genesSizePlot	Man page Source code
geom_flat_violin	Source code
getAllConditions	Man page
getAllConditions,COTAN-method	Man page
getCOTANSlots	Source code
getCells	Man page
getCells,COTAN-method	Man page
getCellsCoex	Man page
getCellsCoex,COTAN-method	Man page
getCellsSize	Man page
getCellsSize,COTAN-method	Man page
getCheckerThreshold	Man page
getCheckerThreshold,AdvancedGDIUniformityCheck-method	Man page
getCheckerThreshold,SimpleGDIUniformityCheck-method	Man page
getClusterizationData	Man page
getClusterizationData,COTAN-method	Man page
getClusterizationName	Man page
getClusterizationName,COTAN-method	Man page
getClusterizations	Man page
getClusterizations,COTAN-method	Man page
getClusters	Man page Source code
getClustersCoex	Man page
getClustersCoex,COTAN-method	Man page
getColorsVector	Man page Source code
getColumnFromDF	Man page Source code
getCondition	Man page
getCondition,COTAN-method	Man page
getConditionName	Man page
getConditionName,COTAN-method	Man page
getDims	Man page
getDims,COTAN-method	Man page
getDispersion	Man page
getDispersion,COTAN-method	Man page
getFullyExpressedGenes	Man page
getFullyExpressedGenes,COTAN-method	Man page
getFullyExpressingCells	Man page
getFullyExpressingCells,COTAN-method	Man page
getGDI	Man page
getGDI,COTAN-method	Man page
getGenes	Man page
getGenes,COTAN-method	Man page
getGenesCoex	Man page
getGenesCoex,COTAN-method	Man page
getGenesSize	Man page
getGenesSize,COTAN-method	Man page
getLambda	Man page
getLambda,COTAN-method	Man page
getLogNormData	Man page Source code
getMetadataCells	Man page
getMetadataCells,COTAN-method	Man page
getMetadataDataset	Man page
getMetadataDataset,COTAN-method	Man page
getMetadataElement	Man page
getMetadataElement,COTAN-method	Man page
getMetadataGenes	Man page
getMetadataGenes,COTAN-method	Man page
getMu	Man page Source code
getNormalizedData	Man page Source code
getNu	Man page
getNu,COTAN-method	Man page
getNuNormData	Man page Source code
getNumCells	Man page
getNumCells,COTAN-method	Man page
getNumExpressedGenes	Man page
getNumExpressedGenes,COTAN-method	Man page
getNumGenes	Man page
getNumGenes,COTAN-method	Man page
getNumOfExpressingCells	Man page
getNumOfExpressingCells,COTAN-method	Man page
getProbabilityOfZero	Man page Source code
getRawData	Man page
getRawData,COTAN-method	Man page
getScCOTANSlots	Source code
getZeroOneProj	Man page
getZeroOneProj,COTAN-method	Man page
groupByClusters	Man page Source code
groupByClustersList	Man page Source code
handleMultiCore	Man page Source code
handleNamesSubsets	Man page Source code
heatmapPlot	Man page Source code
initializeMetaDataset	Man page
initializeMetaDataset,COTAN-method	Man page
isCoexAvailable	Man page
isCoexAvailable,COTAN-method	Man page
isEmptyName	Man page Source code
logFoldChangeOnClusters	Man page Source code
logThis	Man page Source code
mat2vec_rfast	Man page Source code
mergeClusters	Man page Source code
mergeUniformCellsClusters	Man page Source code
mitochondrialPercentagePlot	Man page Source code
multiMergeClusters	Man page Source code
niceFactorLevels	Man page Source code
normalizeNameAndLabels	Man page Source code
nuBisection	Man page Source code
observedContingencyTables	Man page Source code
observedContingencyTablesYY	Man page Source code
observedPartialContingencyTables	Man page Source code
observedPartialContingencyTablesYY	Man page Source code
pValueFromDEA	Man page Source code
parallelDispersionBisection	Man page Source code
parallelNuBisection	Man page Source code
plotTheme	Man page Source code
proceedToCoex	Man page
proceedToCoex,COTAN-method	Man page
raw.dataset	Man page
reorderClusterization	Man page Source code
runDispSolver	Source code
runNuSolver	Source code
runSingleDEA	Source code
scCOTAN-class	Man page
scCotan_coerce_to_COTAN	Man page
scatterPlot	Man page Source code
setColumnInDF	Man page Source code
setLoggingFile	Man page Source code
setLoggingLevel	Man page Source code
seuratClustering	Source code
seuratHVG	Source code
shiftCheckerThresholds	Man page
shiftCheckerThresholds,AdvancedGDIUniformityCheck,numeric-method	Man page
shiftCheckerThresholds,SimpleGDIUniformityCheck,numeric-method	Man page
singleHeatmapDF	Man page Source code
storeGDI	Man page
storeGDI,COTAN-method	Man page
test.dataset	Man page
test.dataset.clusters1	Man page
test.dataset.clusters2	Man page
toClustersList	Man page Source code
updateMetaInfo	Source code
vec2mat_rfast	Man page Source code
vignette.merge.clusters	Man page
vignette.merge2.clusters	Man page
vignette.split.clusters	Man page