NAMESPACE

# Generated by roxygen2: do not edit by hand

export(calcEffectSizes)
export(combineSCE)
export(computeZScore)
export(constructSCE)
export(convertGeneIDs)
export(convertSCEToSeurat)
export(convertSeuratToSCE)
export(discreteColorPalette)
export(distinctColors)
export(downSampleCells)
export(downSampleDepth)
export(enrichRSCE)
export(exportSCE)
export(exportSCEtoAnnData)
export(exportSCEtoFlatFile)
export(featureIndex)
export(findMarkerDiffExp)
export(generateMeta)
export(generateSimulatedData)
export(getBiomarker)
export(getMSigDBTable)
export(getPCA)
export(getSceParams)
export(getTSNE)
export(getTopHVG)
export(getUMAP)
export(gsvaPlot)
export(gsvaSCE)
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(importMultipleSources)
export(importOptimus)
export(importSEQC)
export(importSTARsolo)
export(iterateSimulations)
export(mergeSCEColData)
export(plotBarcodeRankDropsResults)
export(plotBarcodeRankScatter)
export(plotBatchVariance)
export(plotBcdsResults)
export(plotBiomarker)
export(plotCxdsResults)
export(plotDEGHeatmap)
export(plotDEGRegression)
export(plotDEGViolin)
export(plotDecontXResults)
export(plotDoubletCellsResults)
export(plotDoubletFinderResults)
export(plotEmptyDropsResults)
export(plotEmptyDropsScatter)
export(plotMASTThresholdGenes)
export(plotMarkerDiffExp)
export(plotPCA)
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(plotScdsHybridResults)
export(plotScrubletResults)
export(plotTSNE)
export(plotUMAP)
export(qcInputProcess)
export(readSingleCellMatrix)
export(reportCellQC)
export(reportDiffExp)
export(reportDropletQC)
export(reportQCTool)
export(retrieveSCEIndex)
export(runANOVA)
export(runBBKNN)
export(runBarcodeRankDrops)
export(runBcds)
export(runCellQC)
export(runComBat)
export(runCxds)
export(runCxdsBcdsHybrid)
export(runDEAnalysis)
export(runDESeq2)
export(runDecontX)
export(runDoubletCells)
export(runDoubletFinder)
export(runDropletQC)
export(runEmptyDrops)
export(runFastMNN)
export(runHarmony)
export(runKMeans)
export(runLIGER)
export(runLimmaBC)
export(runLimmaDE)
export(runMAST)
export(runMNNCorrect)
export(runPerCellQC)
export(runSCANORAMA)
export(runSCMerge)
export(runScranSNN)
export(runScrublet)
export(runSeurat3Integration)
export(runZINBWaVE)
export(sampleSummaryStats)
export(scater_logNormCounts)
export(scran_modelGeneVar)
export(sctkListGeneSetCollections)
export(sctkPythonInstallConda)
export(sctkPythonInstallVirtualEnv)
export(selectSCTKConda)
export(selectSCTKVirtualEnvironment)
export(seuratComputeHeatmap)
export(seuratComputeJackStraw)
export(seuratElbowPlot)
export(seuratFindClusters)
export(seuratFindHVG)
export(seuratHeatmapPlot)
export(seuratICA)
export(seuratIntegration)
export(seuratJackStrawPlot)
export(seuratNormalizeData)
export(seuratPCA)
export(seuratPlotHVG)
export(seuratReductionPlot)
export(seuratRunTSNE)
export(seuratRunUMAP)
export(seuratSCTransform)
export(seuratScaleData)
export(singleCellTK)
export(subDiffEx)
export(subDiffExANOVA)
export(subDiffExttest)
export(subsetSCECols)
export(subsetSCERows)
export(summarizeSCE)
export(trimCounts)
export(visPlot)
import(Biobase)
import(DelayedArray)
import(DropletUtils)
import(GSVAdata)
import(SingleCellExperiment)
importFrom(SingleCellExperiment,"counts<-")
importFrom(SingleCellExperiment,"reducedDim<-")
importFrom(SingleCellExperiment,counts)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(dplyr,"%>%")
importFrom(dplyr,group_by)
importFrom(dplyr,summarize)
importFrom(magrittr,"%>%")
importFrom(reticulate,import)
importFrom(reticulate,py_module_available)
importFrom(reticulate,py_set_seed)
importFrom(tools,file_ext)