compbiomed/singleCellTK
Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Package index
Search the compbiomed/singleCellTK package
Vignettes
Functions
652
Source code
162
Man pages
237
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compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data
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API

API for compbiomed/singleCellTK
Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Global functions
.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
.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
compbiomed/singleCellTK documentation built on May 8, 2024, 6:58 p.m.

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