Global functions | |
---|---|
COTAN | Man page Source code |
COTAN-Legacy | Man page |
COTAN-class | Man page |
COTANObjectCreation | Man page |
CalculatingCOEX | Man page |
ClustersList | Man page |
DEAOnClusters | Man page Source code |
Datasets | Man page |
ECDPlot | Man page Source code |
ERCCraw | Man page |
GDIPlot | Man page Source code |
GenesStatistics | Man page |
HandleMetaData | Man page |
HandlingClusterizations | Man page |
HandlingConditions | Man page |
HeatmapPlots | Man page |
Installing_torch | Man page |
LoggingFunctions | Man page |
NumericUtilities | Man page |
ParametersEstimations | Man page |
RawDataCleaning | Man page |
RawDataGetters | Man page |
UMAPPlot | Man page Source code |
UniformClusters | 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 |
canUseTorch | 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 |
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 |
contingencyTables | Man page Source code |
datasetTags | 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 | 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 |
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 | Source code |
handleNamesSubsets | Source code |
heatmapPlot | Man page Source code |
initializeMetaDataset | Man page |
initializeMetaDataset,COTAN-method | Man page |
isClusterUniform | Man page Source code |
isCoexAvailable | Man page |
isCoexAvailable,COTAN-method | Man page |
isEmptyName | 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 | 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 | Man page |
scCOTAN-class | 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 |
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.split.clusters | Man page |
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