A B C D E F G H I L M N O P R S T U V
addClusterization | Handling cells' _clusterization_ and related functions |
addClusterization-method | Handling cells' _clusterization_ and related functions |
addClusterizationCoex | Handling cells' _clusterization_ and related functions |
addClusterizationCoex-method | Handling cells' _clusterization_ and related functions |
addCondition | Handling cells' _conditions_ and related functions |
addCondition-method | Handling cells' _conditions_ and related functions |
addElementToMetaDataset | Handling _meta-data_ in 'COTAN' objects |
addElementToMetaDataset-method | Handling _meta-data_ in 'COTAN' objects |
AdvancedGDIUniformityCheck-class | Definition of the *Transcript Uniformity Checker* classes |
asClusterization | _Clusters_ utilities |
automaticCOTANObjectCreation | 'COTAN' shortcuts |
BaseUniformityCheck-class | Definition of the *Transcript Uniformity Checker* classes |
calculateCoex | Calculating the COEX matrix for genes and cells |
calculateCoex-method | Calculating the COEX matrix for genes and cells |
calculateG | Calculating the COEX matrix for genes and cells |
calculateGDI | Calculations of genes statistics |
calculateGDIGivenCorr | Calculations of genes statistics |
calculateGenesCE | Calculations of genes statistics |
calculateLikelihoodOfObserved | Calculating the COEX matrix for genes and cells |
calculateMu | Calculating the COEX matrix for genes and cells |
calculatePartialCoex | Calculating the COEX matrix for genes and cells |
calculatePDI | Calculations of genes statistics |
calculatePValue | Calculations of genes statistics |
calculateS | Calculating the COEX matrix for genes and cells |
calculateThresholdShiftToUniformity | Definition of the *Transcript Uniformity Checker* classes |
calculateThresholdShiftToUniformity-method | Definition of the *Transcript Uniformity Checker* classes |
CalculatingCOEX | Calculating the COEX matrix for genes and cells |
canUseTorch | Handling Multi-Core and GPU environments |
cellsHeatmapPlot | Heatmap Plots |
cellSizePlot | Raw data cleaning |
cellsUMAPPlot | Handling cells' _clusterization_ and related functions |
cellsUniformClustering | Uniform Clusters |
checkClusterUniformity | Uniform Clusters |
checkersToDF | Definition of the *Transcript Uniformity Checker* classes |
checkObjIsUniform | Definition of the *Transcript Uniformity Checker* classes |
checkObjIsUniform-method | Definition of the *Transcript Uniformity Checker* classes |
clean | Raw data cleaning |
clean-method | Raw data cleaning |
cleanPlots | Raw data cleaning |
clusterGeneContingencyTables | Handling cells' _clusterization_ and related functions |
clustersDeltaExpression | Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions |
ClustersList | _Clusters_ utilities |
clustersMarkersHeatmapPlot | Handling cells' _clusterization_ and related functions |
clustersSummaryData | Handling cells' _clusterization_ and related functions |
clustersSummaryPlot | Handling cells' _clusterization_ and related functions |
clustersTreePlot | Handling cells' _clusterization_ and related functions |
conditionsFromNames | Handle names and factors' levels |
contingencyTables | Calculating the COEX matrix for genes and cells |
Conversions | Data class conversions |
convertFromSingleCellExperiment | Data class conversions |
convertToSingleCellExperiment | Data class conversions |
COTAN | 'COTAN' shortcuts |
COTAN-class | Definition of the 'COTAN' class |
COTAN_coerce_to_scCOTAN | Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions |
COTAN_Legacy | Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions |
COTAN_ObjectCreation | 'COTAN' shortcuts |
Datasets | Data-sets |
datasetTags | Handling _meta-data_ in 'COTAN' objects |
DEAOnClusters | Handling cells' _clusterization_ and related functions |
dfToCheckers | Definition of the *Transcript Uniformity Checker* classes |
dispersionBisection | Numeric Utilities |
distancesBetweenClusters | Handling cells' _clusterization_ and related functions |
dropCellsCoex | Calculating the COEX matrix for genes and cells |
dropCellsCoex-method | Calculating the COEX matrix for genes and cells |
dropClusterization | Handling cells' _clusterization_ and related functions |
dropClusterization-method | Handling cells' _clusterization_ and related functions |
dropCondition | Handling cells' _conditions_ and related functions |
dropCondition-method | Handling cells' _conditions_ and related functions |
dropGenesCells | Raw data cleaning |
dropGenesCells-method | Raw data cleaning |
dropGenesCoex | Calculating the COEX matrix for genes and cells |
dropGenesCoex-method | Calculating the COEX matrix for genes and cells |
ECDPlot | Raw data cleaning |
ERCCraw | Data-sets |
establishGenesClusters | Calculations of genes statistics |
estimateDispersionBisection | Estimation of the 'COTAN' model's parameters |
estimateDispersionBisection-method | Estimation of the 'COTAN' model's parameters |
estimateDispersionNuBisection | Estimation of the 'COTAN' model's parameters |
estimateDispersionNuBisection-method | Estimation of the 'COTAN' model's parameters |
estimateDispersionNuNlminb | Estimation of the 'COTAN' model's parameters |
estimateDispersionNuNlminb-method | Estimation of the 'COTAN' model's parameters |
estimateLambdaLinear | Estimation of the 'COTAN' model's parameters |
estimateLambdaLinear-method | Estimation of the 'COTAN' model's parameters |
estimateNuBisection | Estimation of the 'COTAN' model's parameters |
estimateNuBisection-method | Estimation of the 'COTAN' model's parameters |
estimateNuLinear | Estimation of the 'COTAN' model's parameters |
estimateNuLinear-method | Estimation of the 'COTAN' model's parameters |
estimateNuLinearByCluster | Handling cells' _clusterization_ and related functions |
estimateNuLinearByCluster-method | Handling cells' _clusterization_ and related functions |
estimatorsAreReady | Estimation of the 'COTAN' model's parameters |
expectedContingencyTables | Calculating the COEX matrix for genes and cells |
expectedContingencyTablesNN | Calculating the COEX matrix for genes and cells |
expectedPartialContingencyTables | Calculating the COEX matrix for genes and cells |
expectedPartialContingencyTablesNN | Calculating the COEX matrix for genes and cells |
factorToVector | Handle names and factors' levels |
findClustersMarkers | Handling cells' _clusterization_ and related functions |
findFullyExpressedGenes | Raw data cleaning |
findFullyExpressedGenes-method | Raw data cleaning |
findFullyExpressingCells | Raw data cleaning |
findFullyExpressingCells-method | Raw data cleaning |
flagNotFullyExpressedGenes | Raw data cleaning |
flagNotFullyExpressedGenes-method | Raw data cleaning |
flagNotFullyExpressingCells | Raw data cleaning |
flagNotFullyExpressingCells-method | Raw data cleaning |
fromClustersList | _Clusters_ utilities |
funProbZero | Numeric Utilities |
GDICheck-class | Definition of the *Transcript Uniformity Checker* classes |
GDIPlot | Uniform Clusters |
genesCoexSpace | Calculations of genes statistics |
geneSetEnrichment | Handling cells' _clusterization_ and related functions |
genesHeatmapPlot | Heatmap Plots |
genesSizePlot | Raw data cleaning |
GenesStatistics | Calculations of genes statistics |
getAllConditions | Handling cells' _conditions_ and related functions |
getAllConditions-method | Handling cells' _conditions_ and related functions |
getCells | Raw data 'COTAN' accessors |
getCells-method | Raw data 'COTAN' accessors |
getCellsCoex | Calculating the COEX matrix for genes and cells |
getCellsCoex-method | Calculating the COEX matrix for genes and cells |
getCellsSize | Raw data 'COTAN' accessors |
getCellsSize-method | Raw data 'COTAN' accessors |
getCheckerThreshold | Definition of the *Transcript Uniformity Checker* classes |
getCheckerThreshold-method | Definition of the *Transcript Uniformity Checker* classes |
getClusterizationData | Handling cells' _clusterization_ and related functions |
getClusterizationData-method | Handling cells' _clusterization_ and related functions |
getClusterizationName | Handling cells' _clusterization_ and related functions |
getClusterizationName-method | Handling cells' _clusterization_ and related functions |
getClusterizations | Handling cells' _clusterization_ and related functions |
getClusterizations-method | Handling cells' _clusterization_ and related functions |
getClusters | Handling cells' _clusterization_ and related functions |
getClustersCoex | Handling cells' _clusterization_ and related functions |
getClustersCoex-method | Handling cells' _clusterization_ and related functions |
getColorsVector | getColorsVector |
getColumnFromDF | Handling _meta-data_ in 'COTAN' objects |
getCondition | Handling cells' _conditions_ and related functions |
getCondition-method | Handling cells' _conditions_ and related functions |
getConditionName | Handling cells' _conditions_ and related functions |
getConditionName-method | Handling cells' _conditions_ and related functions |
getDims | Handling _meta-data_ in 'COTAN' objects |
getDims-method | Handling _meta-data_ in 'COTAN' objects |
getDispersion | Estimation of the 'COTAN' model's parameters |
getDispersion-method | Estimation of the 'COTAN' model's parameters |
getFullyExpressedGenes | Raw data cleaning |
getFullyExpressedGenes-method | Raw data cleaning |
getFullyExpressingCells | Raw data cleaning |
getFullyExpressingCells-method | Raw data cleaning |
getGDI | Calculations of genes statistics |
getGDI-method | Calculations of genes statistics |
getGenes | Raw data 'COTAN' accessors |
getGenes-method | Raw data 'COTAN' accessors |
getGenesCoex | Calculating the COEX matrix for genes and cells |
getGenesCoex-method | Calculating the COEX matrix for genes and cells |
getGenesSize | Raw data 'COTAN' accessors |
getGenesSize-method | Raw data 'COTAN' accessors |
getLambda | Estimation of the 'COTAN' model's parameters |
getLambda-method | Estimation of the 'COTAN' model's parameters |
getLogNormData | Estimation of the 'COTAN' model's parameters |
getMetadataCells | Handling _meta-data_ in 'COTAN' objects |
getMetadataCells-method | Handling _meta-data_ in 'COTAN' objects |
getMetadataDataset | Handling _meta-data_ in 'COTAN' objects |
getMetadataDataset-method | Handling _meta-data_ in 'COTAN' objects |
getMetadataElement | Handling _meta-data_ in 'COTAN' objects |
getMetadataElement-method | Handling _meta-data_ in 'COTAN' objects |
getMetadataGenes | Handling _meta-data_ in 'COTAN' objects |
getMetadataGenes-method | Handling _meta-data_ in 'COTAN' objects |
getMu | Calculating the COEX matrix for genes and cells |
getNormalizedData | Estimation of the 'COTAN' model's parameters |
getNu | Estimation of the 'COTAN' model's parameters |
getNu-method | Estimation of the 'COTAN' model's parameters |
getNumCells | Raw data 'COTAN' accessors |
getNumCells-method | Raw data 'COTAN' accessors |
getNumExpressedGenes | Raw data 'COTAN' accessors |
getNumExpressedGenes-method | Raw data 'COTAN' accessors |
getNumGenes | Raw data 'COTAN' accessors |
getNumGenes-method | Raw data 'COTAN' accessors |
getNumOfExpressingCells | Raw data 'COTAN' accessors |
getNumOfExpressingCells-method | Raw data 'COTAN' accessors |
getNuNormData | Estimation of the 'COTAN' model's parameters |
getProbabilityOfZero | Estimation of the 'COTAN' model's parameters |
getRawData | Raw data 'COTAN' accessors |
getRawData-method | Raw data 'COTAN' accessors |
getZeroOneProj | Raw data 'COTAN' accessors |
getZeroOneProj-method | Raw data 'COTAN' accessors |
groupByClusters | _Clusters_ utilities |
groupByClustersList | _Clusters_ utilities |
HandleMetaData | Handling _meta-data_ in 'COTAN' objects |
handleMultiCore | Handling Multi-Core and GPU environments |
handleNamesSubsets | Handle names and factors' levels |
HandleStrings | Handle names and factors' levels |
HandlingClusterizations | Handling cells' _clusterization_ and related functions |
HandlingConditions | Handling cells' _conditions_ and related functions |
heatmapPlot | Heatmap Plots |
HeatmapPlots | Heatmap Plots |
initializeMetaDataset | Handling _meta-data_ in 'COTAN' objects |
initializeMetaDataset-method | Handling _meta-data_ in 'COTAN' objects |
Installing_torch | Installing torch R library (on Linux) |
isCoexAvailable | Calculating the COEX matrix for genes and cells |
isCoexAvailable-method | Calculating the COEX matrix for genes and cells |
isEmptyName | Handle names and factors' levels |
logFoldChangeOnClusters | Handling cells' _clusterization_ and related functions |
LoggingFunctions | Logging in the 'COTAN' package |
logThis | Logging in the 'COTAN' package |
mat2vec_rfast | Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions |
mergeClusters | _Clusters_ utilities |
mergeUniformCellsClusters | Uniform Clusters |
mitochondrialPercentagePlot | Raw data cleaning |
multiMergeClusters | _Clusters_ utilities |
MultiThreading | Handling Multi-Core and GPU environments |
niceFactorLevels | Handle names and factors' levels |
normalizeNameAndLabels | Handling cells' _conditions_ and related functions |
nuBisection | Numeric Utilities |
NumericUtilities | Numeric Utilities |
observedContingencyTables | Calculating the COEX matrix for genes and cells |
observedContingencyTablesYY | Calculating the COEX matrix for genes and cells |
observedPartialContingencyTables | Calculating the COEX matrix for genes and cells |
observedPartialContingencyTablesYY | Calculating the COEX matrix for genes and cells |
parallelDispersionBisection | Numeric Utilities |
parallelNuBisection | Numeric Utilities |
ParametersEstimations | Estimation of the 'COTAN' model's parameters |
plotTheme | Heatmap Plots |
proceedToCoex | 'COTAN' shortcuts |
proceedToCoex-method | 'COTAN' shortcuts |
pValueFromDEA | Handling cells' _clusterization_ and related functions |
raw.dataset | Data-sets |
RawDataCleaning | Raw data cleaning |
RawDataGetters | Raw data 'COTAN' accessors |
reorderClusterization | Handling cells' _clusterization_ and related functions |
scatterPlot | Raw data cleaning |
scCOTAN-class | Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions |
scCotan_coerce_to_COTAN | Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions |
screePlot | Raw data cleaning |
setColumnInDF | Handling _meta-data_ in 'COTAN' objects |
setLoggingFile | Logging in the 'COTAN' package |
setLoggingLevel | Logging in the 'COTAN' package |
shiftCheckerThresholds | Definition of the *Transcript Uniformity Checker* classes |
shiftCheckerThresholds-method | Definition of the *Transcript Uniformity Checker* classes |
SimpleGDIUniformityCheck-class | Definition of the *Transcript Uniformity Checker* classes |
singleHeatmapDF | Heatmap Plots |
storeGDI | Calculations of genes statistics |
storeGDI-method | Calculations of genes statistics |
test.dataset | Data-sets |
test.dataset.clusters1 | Data-sets |
test.dataset.clusters2 | Data-sets |
toClustersList | _Clusters_ utilities |
UMAPPlot | Handling cells' _clusterization_ and related functions |
UniformClusters | Uniform Clusters |
UniformTranscriptCheckers | Definition of the *Transcript Uniformity Checker* classes |
vec2mat_rfast | Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions |
vignette.merge.clusters | Data-sets |
vignette.merge2.clusters | Data-sets |
vignette.split.clusters | Data-sets |