| .SoupXOneBatch |
Source code
|
| .addSeuratToMetaDataSCE |
Source code
|
| .bimodality_coefficient |
Source code
|
| .binSCTK |
Source code
|
| .calcMarkerExpr |
Source code
|
| .calculateDEMetrics |
Source code
|
| .cellQC |
Source code
|
| .checkArgsImportCellRanger |
Source code
|
| .checkArgsImportOptimus |
Source code
|
| .checkBCMeta |
Source code
|
| .checkBoth |
Source code
|
| .checkCell |
Source code
|
| .checkDiffExpResultExists |
Source code
|
| .checkDroplet |
Source code
|
| .checkGzip |
Source code
|
| .checkOverwrite |
Source code
|
| .checkSCEValidity |
Source code
|
| .combineColData |
Source code
|
| .combineRowData |
Source code
|
| .computeSignificantPC |
Source code
|
| .constructColdata |
Source code
|
| .constructSCE |
Source code
|
| .constructSCEFromBUStoolsOutputs |
Source code
|
| .constructSCEFromCellRangerOutputs |
Source code
|
| .constructSCEFromOptimusOutputs |
Source code
|
| .constructSCEFromSTARsoloOutputs |
Source code
|
| .constructSCEFromSeqcOutputs |
Source code
|
| .convertFactorToCharacter |
Source code
|
| .convertToHyphen |
Source code
|
| .convertToMatrix |
Source code
|
| .convert_hex_to_int |
Source code
|
| .dfFromHVGMetric |
Source code
|
| .doubletFinder_v3 |
Source code
|
| .exportHTANFlat |
Source code
|
| .extractMetadata |
Source code
|
| .filterDETable |
Source code
|
| .filterRedDims |
Source code
|
| .find.pK |
Source code
|
| .findConservedMarkers |
Source code
|
| .formatDEAList |
Source code
|
| .getCellRangerOutV2 |
Source code
|
| .getClustersLineData |
Source code
|
| .getComponentNames |
Source code
|
| .getDimUnion |
Source code
|
| .getEnrichrDB |
Source code
|
| .getFileExt |
Source code
|
| .getGeneSetCollection |
Source code
|
| .getGeneUnion |
Source code
|
| .getMatUnion |
Source code
|
| .getOutputFolderPath |
Source code
|
| .getSampleNames |
Source code
|
| .getSamplesPaths |
Source code
|
| .getSeuratObject |
Source code
|
| .getSeuratObjectMajorVersion |
Source code
|
| .getSeuratPackageVersion |
Source code
|
| .getVectorized |
Source code
|
| .ggAddLine |
Source code
|
| .ggBar |
Source code
|
| .ggBubble |
Source code
|
| .ggDensity |
Source code
|
| .ggSCTKCombinePlots |
Source code
|
| .ggSCTKTheme |
Source code
|
| .ggScatter |
Source code
|
| .ggSetScaleFactor |
Source code
|
| .ggViolin |
Source code
|
| .heatmapAnnColor |
Source code
|
| .importAnnDataSample |
Source code
|
| .importBUStools |
Source code
|
| .importCellRanger |
Source code
|
| .importDropEstSample |
Source code
|
| .importMetricsCellRanger |
Source code
|
| .importMetricsStarSolo |
Source code
|
| .importOptimus |
Source code
|
| .importSEQC |
Source code
|
| .importSTARsolo |
Source code
|
| .kurtosis |
Source code
|
| .manageCellVar |
Source code
|
| .manageFactor |
Source code
|
| .manageFeatureVar |
Source code
|
| .mergeAnnotationDF |
Source code
|
| .mergeAssaySCE |
Source code
|
| .mergeColDataSCE |
Source code
|
| .mergeMetaSCE |
Source code
|
| .mergeRedimSCE |
Source code
|
| .mergeRowDataSCE |
Source code
|
| .modelHomotypic |
Source code
|
| .onLoad |
Source code
|
| .parallel_paramSweep |
Source code
|
| .paramSweep |
Source code
|
| .parseUseFeatureSubset |
Source code
|
| .plotHeatmapMulti |
Source code
|
| .readBarcodes |
Source code
|
| .readBarcodesSEQC |
Source code
|
| .readDropEstFile |
Source code
|
| .readEmptyDrops |
Source code
|
| .readFeatures |
Source code
|
| .readFeaturesSEQC |
Source code
|
| .readMatrixMM |
Source code
|
| .readMatrixNpz |
Source code
|
| .readMetricsOptimus |
Source code
|
| .relabelClusterBySize |
Source code
|
| .retrieveGeneSetCollection |
Source code
|
| .runBarcodeRankDrops |
Source code
|
| .runCell |
Source code
|
| .runDoubletFinder |
Source code
|
| .runDroplet |
Source code
|
| .runEmptyDrops |
Source code
|
| .sampleSummaryStats |
Source code
|
| .sce2adata |
Source code
|
| .searchBCDefaultInfo |
Source code
|
| .selectSCEMatrix |
Source code
|
| .seuratGetVariableFeatures |
Source code
|
| .seuratInvalidate |
Source code
|
| .skewness |
Source code
|
| .summarizeSweep |
Source code
|
| .testFunctions |
Source code
|
| .unionGeneMatrix |
Source code
|
| .updateAssaySCE |
Source code
|
| .updateAssaySCEFromScanpy |
Source code
|
| .viridisPseudoTimeColor |
Source code
|
| .withSeed |
Source code
|
| .writeAltExps |
Source code
|
| .writeAssays |
Source code
|
| .writeColData |
Source code
|
| .writeMetaData |
Source code
|
| .writeReducedDims |
Source code
|
| .writeRowData |
Source code
|
| .writeSCEFile |
Source code
|
| CellVarColor |
Source code
|
| MitoGenes |
Man page
|
| SEG |
Man page
|
| calcEffectSizes |
Man page
Source code
|
| combineSCE |
Man page
Source code
|
| computeHeatmap |
Man page
Source code
|
| computeZScore |
Man page
Source code
|
| constructSCE |
Man page
Source code
|
| convertSCEToSeurat |
Man page
Source code
|
| convertSeuratToSCE |
Man page
Source code
|
| dedupRowNames |
Man page
Source code
|
| descriptionBCDS |
Source code
|
| descriptionBarcodeRank |
Source code
|
| descriptionCXDS |
Source code
|
| descriptionDecontX |
Source code
|
| descriptionDoubletFinder |
Source code
|
| descriptionEmptyDrops |
Source code
|
| descriptionRunCellQC |
Source code
|
| descriptionRunDropletQC |
Source code
|
| descriptionRunPerCellQC |
Source code
|
| descriptionScDblFinder |
Source code
|
| descriptionScdsHybrid |
Source code
|
| descriptionScrublet |
Source code
|
| descriptionSoupX |
Source code
|
| description_subsetSCECols |
Source code
|
| detectCellOutlier |
Man page
Source code
|
| diffAbundanceFET |
Man page
Source code
|
| discreteColorPalette |
Man page
Source code
|
| distinctColors |
Man page
Source code
|
| downSampleCells |
Man page
Source code
|
| downSampleDepth |
Man page
Source code
|
| expData |
Man page
|
| expData,ANY,character-method |
Man page
|
| expData<- |
Man page
|
| expData<-,ANY,character,CharacterOrNullOrMissing,logical-method |
Man page
|
| expDataNames |
Man page
|
| expDataNames,ANY-method |
Man page
|
| expDeleteDataTag |
Man page
Source code
|
| expSetDataTag |
Man page
Source code
|
| expTaggedData |
Man page
Source code
|
| exportSCE |
Man page
Source code
|
| exportSCEToSeurat |
Man page
Source code
|
| exportSCEtoAnnData |
Man page
Source code
|
| exportSCEtoFlatFile |
Man page
Source code
|
| featureIndex |
Man page
Source code
|
| findMarkerDiffExp |
Man page
Source code
|
| findMarkerTopTable |
Man page
Source code
|
| generateHTANMeta |
Man page
Source code
|
| generateMeta |
Man page
Source code
|
| generateSimulatedData |
Man page
Source code
|
| getBiomarker |
Man page
Source code
|
| getDEGTopTable |
Man page
Source code
|
| getDiffAbundanceResults |
Man page
|
| getDiffAbundanceResults,SingleCellExperiment-method |
Man page
|
| getDiffAbundanceResults<- |
Man page
|
| getDiffAbundanceResults<-,SingleCellExperiment-method |
Man page
|
| getEnrichRResult |
Man page
|
| getEnrichRResult,SingleCellExperiment-method |
Man page
|
| getEnrichRResult<- |
Man page
|
| getEnrichRResult<-,SingleCellExperiment-method |
Man page
|
| getFindMarkerTopTable |
Man page
Source code
|
| getGenesetNamesFromCollection |
Man page
Source code
|
| getMSigDBTable |
Man page
Source code
|
| getPathwayResultNames |
Man page
Source code
|
| getSampleSummaryStatsTable |
Man page
|
| getSampleSummaryStatsTable,SingleCellExperiment-method |
Man page
|
| getSceParams |
Man page
Source code
|
| getSeuratVariableFeatures |
Man page
Source code
|
| getSoupX |
Man page
|
| getSoupX,SingleCellExperiment-method |
Man page
|
| getSoupX<- |
Man page
|
| getSoupX<-,SingleCellExperiment-method |
Man page
|
| getTSCANResults |
Man page
|
| getTSCANResults,SingleCellExperiment-method |
Man page
|
| getTSCANResults<- |
Man page
|
| getTSCANResults<-,SingleCellExperiment-method |
Man page
|
| getTSNE |
Man page
Source code
|
| getTopHVG |
Man page
Source code
|
| getUMAP |
Man page
Source code
|
| importAlevin |
Man page
Source code
|
| importAnnData |
Man page
Source code
|
| importBUStools |
Man page
Source code
|
| importCellRanger |
Man page
Source code
|
| importCellRangerV2 |
Man page
Source code
|
| importCellRangerV2Sample |
Man page
Source code
|
| importCellRangerV3 |
Man page
Source code
|
| importCellRangerV3Sample |
Man page
Source code
|
| importDropEst |
Man page
Source code
|
| importExampleData |
Man page
Source code
|
| importFromFiles |
Man page
Source code
|
| importGeneSetsFromCollection |
Man page
Source code
|
| importGeneSetsFromGMT |
Man page
Source code
|
| importGeneSetsFromList |
Man page
Source code
|
| importGeneSetsFromMSigDB |
Man page
Source code
|
| importMitoGeneSet |
Man page
Source code
|
| importMultipleSources |
Man page
Source code
|
| importOptimus |
Man page
Source code
|
| importSEQC |
Man page
Source code
|
| importSTARsolo |
Man page
Source code
|
| iterateSimulations |
Man page
Source code
|
| listSampleSummaryStatsTables |
Man page
|
| listSampleSummaryStatsTables,SingleCellExperiment-method |
Man page
|
| listTSCANResults |
Man page
|
| listTSCANResults,SingleCellExperiment-method |
Man page
|
| listTSCANTerminalNodes |
Man page
|
| listTSCANTerminalNodes,SingleCellExperiment-method |
Man page
|
| mergeSCEColData |
Man page
Source code
|
| mouseBrainSubsetSCE |
Man page
|
| msigdb_table |
Man page
|
| plotBarcodeRankDropsResults |
Man page
Source code
|
| plotBarcodeRankScatter |
Man page
Source code
|
| plotBatchCorrCompare |
Man page
Source code
|
| plotBatchVariance |
Man page
Source code
|
| plotBcdsResults |
Man page
Source code
|
| plotBubble |
Man page
Source code
|
| plotClusterAbundance |
Man page
Source code
|
| plotCxdsResults |
Man page
Source code
|
| plotDEGHeatmap |
Man page
Source code
|
| plotDEGRegression |
Man page
Source code
|
| plotDEGViolin |
Man page
Source code
|
| plotDEGVolcano |
Man page
Source code
|
| plotDecontXResults |
Man page
Source code
|
| plotDimRed |
Man page
Source code
|
| plotDoubletFinderResults |
Man page
Source code
|
| plotEmptyDropsResults |
Man page
Source code
|
| plotEmptyDropsScatter |
Man page
Source code
|
| plotFindMarkerHeatmap |
Man page
Source code
|
| plotMASTThresholdGenes |
Man page
Source code
|
| plotMarkerDiffExp |
Man page
Source code
|
| plotPCA |
Man page
Source code
|
| plotPathway |
Man page
Source code
|
| plotRunPerCellQCResults |
Man page
Source code
|
| plotSCEBarAssayData |
Man page
Source code
|
| plotSCEBarColData |
Man page
Source code
|
| plotSCEBatchFeatureMean |
Man page
|
| plotSCEDensity |
Man page
Source code
|
| plotSCEDensityAssayData |
Man page
Source code
|
| plotSCEDensityColData |
Man page
Source code
|
| plotSCEDimReduceColData |
Man page
Source code
|
| plotSCEDimReduceFeatures |
Man page
Source code
|
| plotSCEHeatmap |
Man page
Source code
|
| plotSCEScatter |
Man page
Source code
|
| plotSCEViolin |
Man page
Source code
|
| plotSCEViolinAssayData |
Man page
Source code
|
| plotSCEViolinColData |
Man page
Source code
|
| plotScDblFinderResults |
Man page
Source code
|
| plotScanpyDotPlot |
Man page
Source code
|
| plotScanpyEmbedding |
Man page
Source code
|
| plotScanpyHVG |
Man page
Source code
|
| plotScanpyHeatmap |
Man page
Source code
|
| plotScanpyMarkerGenes |
Man page
Source code
|
| plotScanpyMarkerGenesDotPlot |
Man page
Source code
|
| plotScanpyMarkerGenesHeatmap |
Man page
Source code
|
| plotScanpyMarkerGenesMatrixPlot |
Man page
Source code
|
| plotScanpyMarkerGenesViolin |
Man page
Source code
|
| plotScanpyMatrixPlot |
Man page
Source code
|
| plotScanpyPCA |
Man page
Source code
|
| plotScanpyPCAGeneRanking |
Man page
Source code
|
| plotScanpyPCAVariance |
Man page
Source code
|
| plotScanpyViolin |
Man page
Source code
|
| plotScdsHybridResults |
Man page
Source code
|
| plotScrubletResults |
Man page
Source code
|
| plotSeuratElbow |
Man page
Source code
|
| plotSeuratGenes |
Man page
Source code
|
| plotSeuratHVG |
Man page
Source code
|
| plotSeuratHeatmap |
Man page
Source code
|
| plotSeuratJackStraw |
Man page
Source code
|
| plotSeuratReduction |
Man page
Source code
|
| plotSoupXResults |
Man page
Source code
|
| plotTSCANClusterDEG |
Man page
Source code
|
| plotTSCANClusterPseudo |
Man page
Source code
|
| plotTSCANDimReduceFeatures |
Man page
Source code
|
| plotTSCANPseudotimeGenes |
Man page
Source code
|
| plotTSCANPseudotimeHeatmap |
Man page
Source code
|
| plotTSCANResults |
Man page
Source code
|
| plotTSNE |
Man page
Source code
|
| plotTopHVG |
Man page
Source code
|
| plotUMAP |
Man page
Source code
|
| powerCalc |
Source code
|
| qcInputProcess |
Man page
Source code
|
| readSingleCellMatrix |
Man page
Source code
|
| reportCellQC |
Man page
Source code
|
| reportClusterAbundance |
Man page
Source code
|
| reportDiffAbundanceFET |
Man page
Source code
|
| reportDiffExp |
Man page
Source code
|
| reportDropletQC |
Man page
Source code
|
| reportFindMarker |
Man page
Source code
|
| reportQCTool |
Man page
Source code
|
| reportSeurat |
Man page
Source code
|
| reportSeuratClustering |
Man page
Source code
|
| reportSeuratDimRed |
Man page
Source code
|
| reportSeuratFeatureSelection |
Man page
Source code
|
| reportSeuratMarkerSelection |
Man page
Source code
|
| reportSeuratNormalization |
Man page
Source code
|
| reportSeuratResults |
Man page
Source code
|
| reportSeuratRun |
Man page
Source code
|
| reportSeuratScaling |
Man page
Source code
|
| retrieveSCEIndex |
Man page
Source code
|
| runANOVA |
Man page
Source code
|
| runBBKNN |
Man page
Source code
|
| runBarcodeRankDrops |
Man page
Source code
|
| runBcds |
Man page
Source code
|
| runCellQC |
Man page
Source code
|
| runClusterSummaryMetrics |
Man page
Source code
|
| runComBatSeq |
Man page
Source code
|
| runCxds |
Man page
Source code
|
| runCxdsBcdsHybrid |
Man page
Source code
|
| runDEAnalysis |
Man page
Source code
|
| runDESeq2 |
Man page
Source code
|
| runDecontX |
Man page
Source code
|
| runDimReduce |
Man page
Source code
|
| runDoubletFinder |
Man page
Source code
|
| runDropletQC |
Man page
Source code
|
| runEmptyDrops |
Man page
Source code
|
| runEnrichR |
Man page
Source code
|
| runFastMNN |
Man page
Source code
|
| runFeatureSelection |
Man page
Source code
|
| runFindMarker |
Man page
Source code
|
| runGSVA |
Man page
Source code
|
| runHarmony |
Man page
Source code
|
| runKMeans |
Man page
Source code
|
| runLimmaBC |
Man page
Source code
|
| runLimmaDE |
Man page
Source code
|
| runMAST |
Man page
Source code
|
| runMNNCorrect |
Man page
Source code
|
| runModelGeneVar |
Man page
Source code
|
| runNormalization |
Man page
Source code
|
| runPerCellQC |
Man page
Source code
|
| runQuickTSNE |
Man page
Source code
|
| runQuickUMAP |
Man page
Source code
|
| runSCANORAMA |
Man page
Source code
|
| runSCMerge |
Man page
Source code
|
| runScDblFinder |
Man page
Source code
|
| runScanpyFindClusters |
Man page
Source code
|
| runScanpyFindHVG |
Man page
Source code
|
| runScanpyFindMarkers |
Man page
Source code
|
| runScanpyNormalizeData |
Man page
Source code
|
| runScanpyPCA |
Man page
Source code
|
| runScanpyScaleData |
Man page
Source code
|
| runScanpyTSNE |
Man page
Source code
|
| runScanpyUMAP |
Man page
Source code
|
| runScranSNN |
Man page
Source code
|
| runScrublet |
Man page
Source code
|
| runSeuratFindClusters |
Man page
Source code
|
| runSeuratFindHVG |
Man page
Source code
|
| runSeuratFindMarkers |
Man page
Source code
|
| runSeuratHeatmap |
Man page
Source code
|
| runSeuratICA |
Man page
Source code
|
| runSeuratIntegration |
Man page
Source code
|
| runSeuratJackStraw |
Man page
Source code
|
| runSeuratNormalizeData |
Man page
Source code
|
| runSeuratPCA |
Man page
Source code
|
| runSeuratSCTransform |
Man page
Source code
|
| runSeuratScaleData |
Man page
Source code
|
| runSeuratTSNE |
Man page
Source code
|
| runSeuratUMAP |
Man page
Source code
|
| runSingleR |
Man page
Source code
|
| runSoupX |
Man page
Source code
|
| runTSCAN |
Man page
Source code
|
| runTSCANClusterDEAnalysis |
Man page
Source code
|
| runTSCANDEG |
Man page
Source code
|
| runTSNE |
Man page
Source code
|
| runUMAP |
Man page
Source code
|
| runVAM |
Man page
Source code
|
| runWilcox |
Man page
Source code
|
| runZINBWaVE |
Man page
Source code
|
| sampleSummaryStats |
Man page
Source code
|
| scaterCPM |
Man page
Source code
|
| scaterPCA |
Man page
Source code
|
| scaterlogNormCounts |
Man page
Source code
|
| sce |
Man page
|
| sceBatches |
Man page
|
| sctkListGeneSetCollections |
Man page
Source code
|
| sctkPythonInstallConda |
Man page
Source code
|
| sctkPythonInstallVirtualEnv |
Man page
Source code
|
| selectSCTKConda |
Man page
Source code
|
| selectSCTKVirtualEnvironment |
Man page
Source code
|
| setRowNames |
Man page
Source code
|
| setSCTKDisplayRow |
Man page
Source code
|
| setSampleSummaryStatsTable<- |
Man page
|
| setSampleSummaryStatsTable<-,SingleCellExperiment-method |
Man page
|
| setTopHVG |
Man page
Source code
|
| singleCellTK |
Man page
Source code
|
| subDiffEx |
Man page
Source code
|
| subDiffExANOVA |
Man page
Source code
|
| subDiffExttest |
Man page
Source code
|
| subsetSCECols |
Man page
Source code
|
| subsetSCERows |
Man page
Source code
|
| summarizeSCE |
Man page
Source code
|
| trimCounts |
Man page
Source code
|
