# Generated by roxygen2: do not edit by hand

export("expData<-")
export("getDiffAbundanceResults<-")
export("getEnrichRResult<-")
export("getSoupX<-")
export("getTSCANResults<-")
export(calcEffectSizes)
export(combineSCE)
export(computeHeatmap)
export(computeZScore)
export(constructSCE)
export(convertSCEToSeurat)
export(convertSeuratToSCE)
export(dedupRowNames)
export(detectCellOutlier)
export(diffAbundanceFET)
export(discreteColorPalette)
export(distinctColors)
export(downSampleCells)
export(downSampleDepth)
export(expData)
export(expDataNames)
export(expDeleteDataTag)
export(expSetDataTag)
export(expTaggedData)
export(exportSCE)
export(exportSCEToSeurat)
export(exportSCEtoAnnData)
export(exportSCEtoFlatFile)
export(featureIndex)
export(findMarkerDiffExp)
export(findMarkerTopTable)
export(generateHTANMeta)
export(generateMeta)
export(generateSimulatedData)
export(getBiomarker)
export(getDEGTopTable)
export(getDiffAbundanceResults)
export(getEnrichRResult)
export(getFindMarkerTopTable)
export(getGenesetNamesFromCollection)
export(getMSigDBTable)
export(getPathwayResultNames)
export(getSampleSummaryStatsTable)
export(getSceParams)
export(getSeuratVariableFeatures)
export(getSoupX)
export(getTSCANResults)
export(getTSNE)
export(getTopHVG)
export(getUMAP)
export(importAlevin)
export(importAnnData)
export(importBUStools)
export(importCellRanger)
export(importCellRangerV2)
export(importCellRangerV2Sample)
export(importCellRangerV3)
export(importCellRangerV3Sample)
export(importDropEst)
export(importExampleData)
export(importFromFiles)
export(importGeneSetsFromCollection)
export(importGeneSetsFromGMT)
export(importGeneSetsFromList)
export(importGeneSetsFromMSigDB)
export(importMitoGeneSet)
export(importMultipleSources)
export(importOptimus)
export(importSEQC)
export(importSTARsolo)
export(iterateSimulations)
export(listSampleSummaryStatsTables)
export(listTSCANResults)
export(listTSCANTerminalNodes)
export(mergeSCEColData)
export(plotBarcodeRankDropsResults)
export(plotBarcodeRankScatter)
export(plotBatchCorrCompare)
export(plotBatchVariance)
export(plotBcdsResults)
export(plotBubble)
export(plotClusterAbundance)
export(plotCxdsResults)
export(plotDEGHeatmap)
export(plotDEGRegression)
export(plotDEGViolin)
export(plotDEGVolcano)
export(plotDecontXResults)
export(plotDimRed)
export(plotDoubletFinderResults)
export(plotEmptyDropsResults)
export(plotEmptyDropsScatter)
export(plotFindMarkerHeatmap)
export(plotMASTThresholdGenes)
export(plotMarkerDiffExp)
export(plotPCA)
export(plotPathway)
export(plotRunPerCellQCResults)
export(plotSCEBarAssayData)
export(plotSCEBarColData)
export(plotSCEBatchFeatureMean)
export(plotSCEDensity)
export(plotSCEDensityAssayData)
export(plotSCEDensityColData)
export(plotSCEDimReduceColData)
export(plotSCEDimReduceFeatures)
export(plotSCEHeatmap)
export(plotSCEScatter)
export(plotSCEViolin)
export(plotSCEViolinAssayData)
export(plotSCEViolinColData)
export(plotScDblFinderResults)
export(plotScanpyDotPlot)
export(plotScanpyEmbedding)
export(plotScanpyHVG)
export(plotScanpyHeatmap)
export(plotScanpyMarkerGenes)
export(plotScanpyMarkerGenesDotPlot)
export(plotScanpyMarkerGenesHeatmap)
export(plotScanpyMarkerGenesMatrixPlot)
export(plotScanpyMarkerGenesViolin)
export(plotScanpyMatrixPlot)
export(plotScanpyPCA)
export(plotScanpyPCAGeneRanking)
export(plotScanpyPCAVariance)
export(plotScanpyViolin)
export(plotScdsHybridResults)
export(plotScrubletResults)
export(plotSeuratElbow)
export(plotSeuratGenes)
export(plotSeuratHVG)
export(plotSeuratHeatmap)
export(plotSeuratJackStraw)
export(plotSeuratReduction)
export(plotSoupXResults)
export(plotTSCANClusterDEG)
export(plotTSCANClusterPseudo)
export(plotTSCANDimReduceFeatures)
export(plotTSCANPseudotimeGenes)
export(plotTSCANPseudotimeHeatmap)
export(plotTSCANResults)
export(plotTSNE)
export(plotTopHVG)
export(plotUMAP)
export(qcInputProcess)
export(readSingleCellMatrix)
export(reportCellQC)
export(reportClusterAbundance)
export(reportDiffAbundanceFET)
export(reportDiffExp)
export(reportDropletQC)
export(reportFindMarker)
export(reportQCTool)
export(reportSeurat)
export(reportSeuratClustering)
export(reportSeuratDimRed)
export(reportSeuratFeatureSelection)
export(reportSeuratMarkerSelection)
export(reportSeuratNormalization)
export(reportSeuratResults)
export(reportSeuratRun)
export(reportSeuratScaling)
export(retrieveSCEIndex)
export(runANOVA)
export(runBBKNN)
export(runBarcodeRankDrops)
export(runBcds)
export(runCellQC)
export(runClusterSummaryMetrics)
export(runComBatSeq)
export(runCxds)
export(runCxdsBcdsHybrid)
export(runDEAnalysis)
export(runDESeq2)
export(runDecontX)
export(runDimReduce)
export(runDoubletFinder)
export(runDropletQC)
export(runEmptyDrops)
export(runEnrichR)
export(runFastMNN)
export(runFeatureSelection)
export(runFindMarker)
export(runGSVA)
export(runHarmony)
export(runKMeans)
export(runLimmaBC)
export(runLimmaDE)
export(runMAST)
export(runMNNCorrect)
export(runModelGeneVar)
export(runNormalization)
export(runPerCellQC)
export(runQuickTSNE)
export(runQuickUMAP)
export(runSCANORAMA)
export(runSCMerge)
export(runScDblFinder)
export(runScanpyFindClusters)
export(runScanpyFindHVG)
export(runScanpyFindMarkers)
export(runScanpyNormalizeData)
export(runScanpyPCA)
export(runScanpyScaleData)
export(runScanpyTSNE)
export(runScanpyUMAP)
export(runScranSNN)
export(runScrublet)
export(runSeuratFindClusters)
export(runSeuratFindHVG)
export(runSeuratFindMarkers)
export(runSeuratHeatmap)
export(runSeuratICA)
export(runSeuratIntegration)
export(runSeuratJackStraw)
export(runSeuratNormalizeData)
export(runSeuratPCA)
export(runSeuratSCTransform)
export(runSeuratScaleData)
export(runSeuratTSNE)
export(runSeuratUMAP)
export(runSingleR)
export(runSoupX)
export(runTSCAN)
export(runTSCANClusterDEAnalysis)
export(runTSCANDEG)
export(runTSNE)
export(runUMAP)
export(runVAM)
export(runWilcox)
export(runZINBWaVE)
export(sampleSummaryStats)
export(scaterCPM)
export(scaterPCA)
export(scaterlogNormCounts)
export(sctkListGeneSetCollections)
export(sctkPythonInstallConda)
export(sctkPythonInstallVirtualEnv)
export(selectSCTKConda)
export(selectSCTKVirtualEnvironment)
export(setRowNames)
export(setSCTKDisplayRow)
export(setTopHVG)
export(singleCellTK)
export(subDiffEx)
export(subDiffExANOVA)
export(subDiffExttest)
export(subsetSCECols)
export(subsetSCERows)
export(summarizeSCE)
export(trimCounts)
exportMethods("expData<-")
exportMethods("getDiffAbundanceResults<-")
exportMethods("getEnrichRResult<-")
exportMethods("getSoupX<-")
exportMethods("getTSCANResults<-")
exportMethods(expData)
exportMethods(expDataNames)
exportMethods(getDiffAbundanceResults)
exportMethods(getEnrichRResult)
exportMethods(getSoupX)
exportMethods(getTSCANResults)
exportMethods(listTSCANResults)
exportMethods(listTSCANTerminalNodes)
import(Biobase)
import(DelayedArray)
import(DropletUtils)
import(GSVAdata)
import(SingleCellExperiment)
import(eds)
importFrom(BiocParallel,SerialParam)
importFrom(ComplexHeatmap,anno_barplot)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(SingleCellExperiment,"counts<-")
importFrom(SingleCellExperiment,"reducedDim<-")
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,altExp)
importFrom(SingleCellExperiment,counts)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,reducedDimNames)
importFrom(SingleCellExperiment,reducedDims)
importFrom(SingleCellExperiment,rowSubset)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"assayNames<-")
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,count)
importFrom(dplyr,desc)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,one_of)
importFrom(dplyr,select)
importFrom(dplyr,summarize)
importFrom(dplyr,ungroup)
importFrom(grid,gpar)
importFrom(magrittr,"%>%")
importFrom(methods,slot)
importFrom(reshape2,melt)
importFrom(reticulate,import)
importFrom(reticulate,py_module_available)
importFrom(reticulate,py_set_seed)
importFrom(rlang,.data)
importFrom(scuttle,aggregateAcrossCells)
importFrom(scuttle,aggregateAcrossFeatures)
importFrom(stats,filter)
importFrom(stats,prcomp)
importFrom(stats,quantile)
importFrom(stringr,str_c)
importFrom(stringr,str_replace_all)
importFrom(tibble,column_to_rownames)
importFrom(tibble,remove_rownames)
importFrom(tibble,tibble)
importFrom(tidyr,spread)
importFrom(tidyr,unite)
importFrom(tools,file_ext)
importFrom(utils,head)
importFrom(utils,packageVersion)
