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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(adaptSpillmat)
export(applyCutoffs)
export(assignPrelim)
export(channels)
export(clrDR)
export(cluster)
export(cluster_codes)
export(cluster_ids)
export(compCytof)
export(computeSpillmat)
export(delta_area)
export(ei)
export(estCutoffs)
export(extractClusters)
export(filterSCE)
export(guessPanel)
export(marker_classes)
export(mergeClusters)
export(n_cells)
export(normCytof)
export(pbMDS)
export(plotAbundances)
export(plotClusterExprs)
export(plotClusterHeatmap)
export(plotCodes)
export(plotCounts)
export(plotDR)
export(plotDiffHeatmap)
export(plotEvents)
export(plotExprHeatmap)
export(plotExprs)
export(plotFreqHeatmap)
export(plotMahal)
export(plotMedExprs)
export(plotMultiHeatmap)
export(plotNRS)
export(plotPbExprs)
export(plotScatter)
export(plotSpillmat)
export(plotYields)
export(prepData)
export(runDR)
export(sample_ids)
export(sce2fcs)
export(state_markers)
export(type_markers)
import(ComplexHeatmap)
import(ConsensusClusterPlus)
import(ggplot2)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(ComplexHeatmap,row_anno_text)
importFrom(FlowSOM,BuildSOM)
importFrom(FlowSOM,ReadInput)
importFrom(Matrix,colMeans)
importFrom(Matrix,colSums)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,solve)
importFrom(RColorBrewer,brewer.pal)
importFrom(Rtsne,Rtsne)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(SingleCellExperiment,"int_colData<-")
importFrom(SingleCellExperiment,"int_metadata<-")
importFrom(SingleCellExperiment,"reducedDim<-")
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,colData)
importFrom(SingleCellExperiment,int_colData)
importFrom(SingleCellExperiment,int_metadata)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,reducedDimNames)
importFrom(SingleCellExperiment,reducedDims)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(circlize,colorRamp2)
importFrom(cowplot,get_legend)
importFrom(cowplot,plot_grid)
importFrom(data.table,data.table)
importFrom(dplyr,"%>%")
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,bind_rows)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_all)
importFrom(dplyr,mutate_at)
importFrom(dplyr,mutate_if)
importFrom(dplyr,rename)
importFrom(dplyr,row_number)
importFrom(dplyr,select)
importFrom(dplyr,select_if)
importFrom(dplyr,summarise_if)
importFrom(dplyr,summarize_all)
importFrom(drc,LL.3)
importFrom(drc,drm)
importFrom(flowCore,"exprs<-")
importFrom(flowCore,"identifier<-")
importFrom(flowCore,"keyword<-")
importFrom(flowCore,colnames)
importFrom(flowCore,compensate)
importFrom(flowCore,exprs)
importFrom(flowCore,flowFrame)
importFrom(flowCore,flowSet)
importFrom(flowCore,fsApply)
importFrom(flowCore,identifier)
importFrom(flowCore,isFCSfile)
importFrom(flowCore,keyword)
importFrom(flowCore,parameters)
importFrom(flowCore,read.FCS)
importFrom(flowCore,read.flowSet)
importFrom(flowCore,write.FCS)
importFrom(ggrepel,geom_label_repel)
importFrom(ggrepel,geom_text_repel)
importFrom(ggridges,geom_density_ridges)
importFrom(ggridges,theme_ridges)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,hcl.colors)
importFrom(grDevices,pdf)
importFrom(graphics,hist)
importFrom(graphics,plot)
importFrom(grid,gpar)
importFrom(grid,grid.text)
importFrom(grid,unit)
importFrom(gridExtra,grid.arrange)
importFrom(magrittr,set_colnames)
importFrom(magrittr,set_rownames)
importFrom(matrixStats,colAnys)
importFrom(matrixStats,colMaxs)
importFrom(matrixStats,colMins)
importFrom(matrixStats,colQuantiles)
importFrom(matrixStats,rowMads)
importFrom(matrixStats,rowMaxs)
importFrom(matrixStats,rowMedians)
importFrom(matrixStats,rowMins)
importFrom(matrixStats,rowQuantiles)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(nnls,nnls)
importFrom(purrr,map)
importFrom(purrr,map_depth)
importFrom(reshape2,melt)
importFrom(scales,scientific)
importFrom(scater,calculateDiffusionMap)
importFrom(scater,calculateMDS)
importFrom(scater,calculatePCA)
importFrom(scater,calculateTSNE)
importFrom(scater,calculateUMAP)
importFrom(scater,runDiffusionMap)
importFrom(scater,runMDS)
importFrom(scater,runPCA)
importFrom(scater,runTSNE)
importFrom(scater,runUMAP)
importFrom(stats,D)
importFrom(stats,approx)
importFrom(stats,coef)
importFrom(stats,cov)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,mahalanobis)
importFrom(stats,median)
importFrom(stats,prcomp)
importFrom(stats,predict)
importFrom(stats,quantile)
importFrom(stats,reformulate)
importFrom(stats,runmed)
importFrom(stats,setNames)