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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export("%<-%")
export("%>%")
export(IdentName)
export(NormFindVarFeatScaleData)
export(addQCfilter)
export(addQCmetrics)
export(convertClID2Name)
export(demuxAntibodyData)
export(extractGeneCorrectionsSoupX)
export(extractTopRefMapResults)
export(featureHeatmapByCluster)
export(filterLowGenes)
export(findSoupXFiles)
export(gcoreVlnPlot)
export(gcoreVlnPlot_facetted)
export(generate_capture_QC_cutoffs)
export(getTopNGenesSC)
export(integrate_harmony)
export(integrate_seurat)
export(integrate_stacas)
export(mastWaldTest)
export(plotClusterAnnotTile)
export(plotIntegrationDiagnostics)
export(plotPCAs)
export(plotQCRidgesJoint)
export(plotQC_ADTbinline)
export(plotQC_joint)
export(plotQC_ridges)
export(plotQueryRefMarkerHeatmaps)
export(plotRefMapScoresFacet)
export(plotSoupXGeneAdjustments)
export(plotUMAP_split)
export(plotUmapIntegrated)
export(plot_smaller)
export(prepare_MAST_obj)
export(readCounts10x)
export(readCountsBD)
export(read_excel_allsheets)
export(removeDFDoublets)
export(runIntegration)
export(runSingleR)
export(runSoupX)
export(run_scDblFinder)
export(scoreCC)
export(subset_seurat_object)
export(update_sc)
export(writeDGEResults)
import(Seurat)
import(SingleR)
import(SoupX)
import(dplyr)
import(ggplot2)
import(grDevices)
import(openxlsx)
import(scDblFinder)
importFrom(Matrix,rowSums)
importFrom(S4Vectors,mcols)
importFrom(Seurat,CreateAssayObject)
importFrom(Seurat,CreateSeuratObject)
importFrom(Seurat,Read10X)
importFrom(Seurat,Read10X_h5)
importFrom(Seurat,as.SingleCellExperiment)
importFrom(SoupX,setDR)
importFrom(SummarizedExperiment,assays)
importFrom(clustree,clustree)
importFrom(forcats,fct_rev)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,scale_color_gradient)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,stat_smooth)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplotify,as.ggplot)
importFrom(gtools,mixedsort)
importFrom(here,here)
importFrom(magrittr,"%>%")
importFrom(methods,show)
importFrom(pheatmap,pheatmap)
importFrom(plotly,ggplotly)
importFrom(plyr,mapvalues)
importFrom(rlang,":=")
importFrom(rlang,.data)
importFrom(scater,logNormCounts)
importFrom(scran,findMarkers)
importFrom(stats,density)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,drop_na)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(utils,tail)
importFrom(viridis,scale_fill_viridis)
importFrom(zeallot,"%<-%")