NAMESPACE

# Generated by roxygen2: do not edit by hand

export(AddNewMetaColumn)
export(AppendCiteSeq)
export(AppendPerCellSaturation)
export(AppendPerCellSaturationInBulk)
export(AvgExpression)
export(CalculateClusterEnrichment)
export(CalculatePercentMito)
export(CalculateTcrDiversity)
export(CalculateTcrDiversityFromSeurat)
export(CalculateUcellPerFeature)
export(CellCycleScoring_UCell)
export(CiteSeqDimRedux.Dist)
export(CiteSeqDimRedux.PCA)
export(ClrNormalizeByGroup)
export(ClusteredDotPlot)
export(ConstructEnrichmentDataFrameAndDoStatistics)
export(CreateSeuratObj)
export(DesignModelMatrix)
export(DetectCellStructuresBasedOnCellType)
export(DoLdaParameterScan)
export(DownsampleSeurat)
export(FeaturePlotAcrossReductions)
export(FilterCloneNames)
export(FilterPseudobulkContrasts)
export(FilterRawCounts)
export(FindClustersAndDimRedux)
export(FindDoublets)
export(Find_Markers)
export(FitRegularizedClassificationGlm)
export(GetAssayMetadataSlotName)
export(GetChiDF)
export(GetG2MGenes)
export(GetGeneIds)
export(GetSPhaseGenes)
export(GetSeed)
export(GetXYDataFromPlot)
export(HasSplitLayers)
export(HighlightCellsOnSeuratPlot)
export(InspectSeurat)
export(LogNormalizeUsingAlternateAssay)
export(MakeEnrichmentDotPlot)
export(MergeSeuratObjs)
export(MergeSplitLayers)
export(NanoString_Housekeeping_Normalization)
export(NormalizeAndScale)
export(PerformDifferentialExpression)
export(PerformGlmFit)
export(PerformIntegration)
export(PlotAverageAdtCounts)
export(PlotSdaCellScores)
export(PlotSeuratVariables)
export(PlotTfData)
export(Plot_SDAScoresPerFeature)
export(PredictScTourPseudotime)
export(PseudobulkSeurat)
export(PseudobulkingBarPlot)
export(PseudobulkingDEHeatmap)
export(Q3_Normalization)
export(QuantifyTcrClones)
export(RLE_Plot)
export(RUVg_Housekeeping_Normalization)
export(ReadAndFilter10xData)
export(RegressCellCycle)
export(RenameUsingCD)
export(ResolveLocGenes)
export(RunCoNGA)
export(RunCsCore)
export(RunDecoupleR)
export(RunEscape)
export(RunFilteredContrasts)
export(RunPHATE)
export(RunPcaSteps)
export(RunSDA)
export(RunSeuratWnn)
export(RunSingleR)
export(RunUmapOnSDA)
export(SDAToSeuratMetadata)
export(SDAToSeuratReduction)
export(SDA_GO_Enrichment)
export(ScaleFeaturesIfNeeded)
export(ScoreCellCycle)
export(SetSeed)
export(SeuratToCoNGA)
export(SpatialNormalizeByGroup)
export(SplitSeurat)
export(SubsetSeurat)
export(TrainSctourModel)
export(UpdateMacaqueMmul10NcbiGeneSymbols)
export(WriteCellBarcodes)
export(WriteSummaryMetrics)
export(runLDA)
import(DESeq2)
import(MAST)
import(Seurat)
import(SingleR)
import(dplyr)
import(ggplot2)
import(mlr3verse)
import(patchwork)
importFrom(DropletUtils,barcodeRanks)
importFrom(Matrix,colSums)
importFrom(Seurat,Read10X)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,coalesce)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,top_n)
importFrom(graphics,abline)
importFrom(graphics,boxplot)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,segments)
importFrom(jsonlite,write_json)
importFrom(magrittr,"%>%")
importFrom(methods,"slot<-")
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(mlr3,as_task_classif)
importFrom(mlr3,lrn)
importFrom(mlr3,partition)
importFrom(rlang,":=")
importFrom(scuttle,logNormCounts)
importFrom(stats,approxfun)
importFrom(stats,cmdscale)
importFrom(stats,coef)
importFrom(stats,cor)
importFrom(stats,dist)
importFrom(stats,kmeans)
importFrom(stats,lm)
importFrom(stats,na.omit)
importFrom(stats,prcomp)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,wilcox.test)
importFrom(utils,head)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(utils,tail)
importFrom(utils,write.csv)
importFrom(utils,write.table)