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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(adaptSpillmat)
export(applyCutoffs)
export(assignPrelim)
export(bc_ids)
export(bc_key)
export(cluster)
export(cluster_codes)
export(cluster_ids)
export(compCytof)
export(computeSpillmat)
export(concatFCS)
export(counts)
export(daFrame)
export(deltas)
export(estCutoffs)
export(extractClusters)
export(guessPanel)
export(launchGUI)
export(marker_classes)
export(mergeClusters)
export(mhl_cutoff)
export(mhl_dists)
export(n_cells)
export(normCytof)
export(normed_bcs)
export(outFCS)
export(outFrames)
export(plotAbundances)
export(plotClusterExprs)
export(plotClusterHeatmap)
export(plotCodes)
export(plotCounts)
export(plotDiffHeatmap)
export(plotEvents)
export(plotExprHeatmap)
export(plotExprs)
export(plotMDS)
export(plotMahal)
export(plotMedExprs)
export(plotNRS)
export(plotSNE)
export(plotSpillmat)
export(plotYields)
export(sample_ids)
export(sep_cutoffs)
export(state_markers)
export(tSNE)
export(type_markers)
export(yields)
exportClasses(daFrame)
exportClasses(dbFrame)
exportMethods("mhl_cutoff<-")
exportMethods("sep_cutoffs<-")
exportMethods(exprs)
exportMethods(filter)
exportMethods(outFCS)
exportMethods(outFrames)
import(ComplexHeatmap)
import(ConsensusClusterPlus)
import(Rtsne)
import(SummarizedExperiment)
import(ggplot2)
import(ggrepel)
import(grid)
import(gridExtra)
import(shinydashboard)
importFrom(Biobase,exprs)
importFrom(DT,dataTableOutput)
importFrom(DT,datatable)
importFrom(DT,formatStyle)
importFrom(DT,renderDataTable)
importFrom(FlowSOM,BuildSOM)
importFrom(FlowSOM,ReadInput)
importFrom(Matrix,colSums)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,metadata)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(circlize,colorRamp2)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,count)
importFrom(dplyr,filter)
importFrom(dplyr,funs)
importFrom(dplyr,group_by)
importFrom(dplyr,group_by_)
importFrom(dplyr,mutate_all)
importFrom(dplyr,select)
importFrom(dplyr,summarise_all)
importFrom(dplyr,summarise_at)
importFrom(dplyr,summarize_all)
importFrom(drc,LL.3)
importFrom(drc,drm)
importFrom(flowCore,"description<-")
importFrom(flowCore,"exprs<-")
importFrom(flowCore,"identifier<-")
importFrom(flowCore,colnames)
importFrom(flowCore,compensate)
importFrom(flowCore,description)
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(ggridges,geom_density_ridges)
importFrom(ggridges,theme_ridges)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(graphics,hist)
importFrom(graphics,plot)
importFrom(gridExtra,arrangeGrob)
importFrom(gridExtra,grid.arrange)
importFrom(htmltools,div)
importFrom(htmltools,save_html)
importFrom(limma,plotMDS)
importFrom(magrittr,"%>%")
importFrom(matrixStats,colMaxs)
importFrom(matrixStats,colMins)
importFrom(matrixStats,colQuantiles)
importFrom(matrixStats,rowMaxs)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(nnls,nnls)
importFrom(plotly,config)
importFrom(plotly,ggplotly)
importFrom(plotly,hide_legend)
importFrom(plotly,layout)
importFrom(reshape2,acast)
importFrom(reshape2,melt)
importFrom(scales,hue_pal)
importFrom(shiny,runApp)
importFrom(shinyBS,bsButton)
importFrom(shinyBS,bsPopover)
importFrom(shinyjs,disable)
importFrom(shinyjs,extendShinyjs)
importFrom(shinyjs,hide)
importFrom(shinyjs,useShinyjs)
importFrom(stats,D)
importFrom(stats,approx)
importFrom(stats,coef)
importFrom(stats,cov)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,mad)
importFrom(stats,mahalanobis)
importFrom(stats,median)
importFrom(stats,prcomp)
importFrom(stats,predict)
importFrom(stats,quantile)
importFrom(stats,runmed)
importFrom(stats,setNames)
importFrom(stats,smooth.spline)
importFrom(tidyr,complete)
importFrom(utils,read.csv)
importMethodsFrom(S4Vectors,metadata)