COexpression Tables ANalysis
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Documentation for package ‘COTAN’ version 2.7.4
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A B C D E F G H I L M N O P R S T U V
-- A --
| 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 |
-- B --
| BaseUniformityCheck-class | Definition of the *Transcript Uniformity Checker* classes |
-- C --
| 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 |
-- D --
| 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 |
-- E --
| 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 |
-- F --
| 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 |
-- G --
| 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 |
-- H --
| 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 |
-- I --
| 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 |
-- L --
| logFoldChangeOnClusters | Handling cells' _clusterization_ and related functions |
| LoggingFunctions | Logging in the 'COTAN' package |
| logThis | Logging in the 'COTAN' package |
-- M --
| 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 |
-- N --
| niceFactorLevels | Handle names and factors' levels |
| normalizeNameAndLabels | Handling cells' _conditions_ and related functions |
| nuBisection | Numeric Utilities |
| NumericUtilities | Numeric Utilities |
-- O --
| 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 |
-- P --
| 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 |
-- R --
| raw.dataset | Data-sets |
| RawDataCleaning | Raw data cleaning |
| RawDataGetters | Raw data 'COTAN' accessors |
| reorderClusterization | Handling cells' _clusterization_ and related functions |
-- S --
| 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 |
-- T --
| test.dataset | Data-sets |
| test.dataset.clusters1 | Data-sets |
| test.dataset.clusters2 | Data-sets |
| toClustersList | _Clusters_ utilities |
-- U --
| UMAPPlot | Handling cells' _clusterization_ and related functions |
| UniformClusters | Uniform Clusters |
| UniformTranscriptCheckers | Definition of the *Transcript Uniformity Checker* classes |
-- V --
| 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 |