API for singleCellTK
Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data
| Global functions | |
|---|---|
| .addSeuratToMetaDataSCE | Man page Source code |
| .bimodality_coefficient | Source code |
| .binSCTK | Source code |
| .checkArgsImportCellRanger | Source code |
| .checkArgsImportOptimus | Source code |
| .checkDiffExpResultExists | Man page Source code |
| .checkGzip | Source code |
| .checkOverwrite | Source code |
| .combineColData | Source code |
| .combineRowData | Source code |
| .computeSignificantPC | Man page 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 |
| .convertToMatrix | Source code |
| .doubletFinder_v3 | Source code |
| .extractMetadata | Source code |
| .extractSCEAnnotation | Man page Source code |
| .find.pK | Source code |
| .formatDEAList | Man page Source code |
| .getCellRangerOutV2 | Source code |
| .getComponentNames | Man page Source code |
| .getDimUnion | Source code |
| .getFileExt | Source code |
| .getGeneUnion | Source code |
| .getMatUnion | Source code |
| .getOutputFolderPath | Source code |
| .getSampleNames | Source code |
| .getSamplesPaths | Source code |
| .getVectorized | Source code |
| .ggBar | Man page Source code |
| .ggDensity | Man page Source code |
| .ggSCTKCombinePlots | Source code |
| .ggSCTKTheme | Source code |
| .ggScatter | Man page Source code |
| .ggViolin | Man page Source code |
| .importAnnDataSample | Source code |
| .importBUStools | Source code |
| .importCellRanger | Source code |
| .importDropEstSample | Source code |
| .importOptimus | Source code |
| .importSEQC | Source code |
| .importSTARsolo | Source code |
| .manageFactor | 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 |
| .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 |
| .retrieveGeneSetCollection | Source code |
| .runBarcodeRankDrops | Source code |
| .runDoubletFinder | Source code |
| .runEmptyDrops | Source code |
| .sampleSummaryStats | Source code |
| .sce2adata | Man page Source code |
| .seuratGetVariableFeatures | Man page Source code |
| .seuratInvalidate | Man page Source code |
| .skewness | Source code |
| .summarizeSweep | Source code |
| .testFunctions | Source code |
| .unionGeneMatrix | Source code |
| .updateAssaySCE | Man page Source code |
| .writeAltExps | Source code |
| .writeAssays | Source code |
| .writeColData | Source code |
| .writeMetaData | Source code |
| .writeReducedDims | Source code |
| .writeRowData | Source code |
| .writeSCEFile | Source code |
| SEG | Man page |
| calcEffectSizes | Man page Source code |
| combineSCE | Man page Source code |
| computeZScore | Man page Source code |
| constructSCE | Man page Source code |
| convertGeneIDs | Man page Source code |
| convertSCEToSeurat | Man page Source code |
| convertSeuratToSCE | Man page Source code |
| dataAnnotationColor | Man page Source code |
| descriptionBCDS | Source code |
| descriptionBarcodeRank | Source code |
| descriptionCXDS | Source code |
| descriptionDecontX | Source code |
| descriptionDoubletCells | Source code |
| descriptionDoubletFinder | Source code |
| descriptionEmptyDrops | Source code |
| descriptionRunCellQC | Source code |
| descriptionRunDropletQC | Source code |
| descriptionRunPerCellQC | Source code |
| descriptionScdsHybrid | Source code |
| descriptionScrublet | Source code |
| description_subsetSCECols | Source code |
| discreteColorPalette | Man page Source code |
| distinctColors | Man page Source code |
| downSampleCells | Man page Source code |
| downSampleDepth | Man page Source code |
| enrichRSCE | Man page Source code |
| exportSCE | Man page Source code |
| exportSCEtoAnnData | Man page Source code |
| exportSCEtoFlatFile | Man page Source code |
| featureIndex | Man page Source code |
| featureNameDedup | Source code |
| findMarkerDiffExp | Man page Source code |
| generateMeta | Man page Source code |
| generateSimulatedData | Man page Source code |
| getBiomarker | Man page Source code |
| getMSigDBTable | Man page Source code |
| getPCA | Man page Source code |
| getSceParams | Man page Source code |
| getTSNE | Man page Source code |
| getTopHVG | Man page Source code |
| getUMAP | Man page Source code |
| gsvaPlot | Man page Source code |
| gsvaSCE | 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 |
| 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 |
| mergeSCEColData | Man page Source code |
| mouseBrainSubsetSCE | Man page |
| msigdb_table | Man page |
| plotBarcodeRankDropsResults | Man page Source code |
| plotBarcodeRankScatter | Man page Source code |
| plotBatchVariance | Man page Source code |
| plotBcdsResults | Man page Source code |
| plotBiomarker | Man page Source code |
| plotCxdsResults | Man page Source code |
| plotDEGHeatmap | Man page Source code |
| plotDEGRegression | Man page Source code |
| plotDEGViolin | Man page Source code |
| plotDecontXResults | Man page Source code |
| plotDoubletCellsResults | Man page Source code |
| plotDoubletFinderResults | Man page Source code |
| plotEmptyDropsResults | Man page Source code |
| plotEmptyDropsScatter | Man page Source code |
| plotMASTThresholdGenes | Man page Source code |
| plotMarkerDiffExp | Man page Source code |
| plotPCA | 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 |
| plotScdsHybridResults | Man page Source code |
| plotScrubletResults | Man page Source code |
| plotTSNE | 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 |
| reportDiffExp | Man page Source code |
| reportDropletQC | Man page Source code |
| reportQCTool | 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 |
| runComBat | 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 |
| runDoubletCells | Man page Source code |
| runDoubletFinder | Man page Source code |
| runDropletQC | Man page Source code |
| runEmptyDrops | Man page Source code |
| runFastMNN | 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 |
| runPerCellQC | Man page Source code |
| runSCANORAMA | Man page Source code |
| runSCMerge | Man page Source code |
| runScranSNN | Man page Source code |
| runScrublet | Man page Source code |
| runZINBWaVE | Man page Source code |
| sampleSummaryStats | Man page Source code |
| scater_logNormCounts | Man page Source code |
| sce | Man page |
| sceBatches | Man page |
| scran_modelGeneVar | Man page Source code |
| 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 |
| seuratComputeHeatmap | Man page Source code |
| seuratComputeJackStraw | Man page Source code |
| seuratElbowPlot | Man page Source code |
| seuratFindClusters | Man page Source code |
| seuratFindHVG | Man page Source code |
| seuratHeatmapPlot | Man page Source code |
| seuratICA | Man page Source code |
| seuratIntegration | Man page Source code |
| seuratJackStrawPlot | Man page Source code |
| seuratNormalizeData | Man page Source code |
| seuratPCA | Man page Source code |
| seuratPlotHVG | Man page Source code |
| seuratReductionPlot | Man page Source code |
| seuratRunTSNE | Man page Source code |
| seuratRunUMAP | Man page Source code |
| seuratSCTransform | Man page Source code |
| seuratScaleData | Man page Source code |
| simpleLog | Man page |
| 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 |
| visPlot | Man page Source code |
