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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(batchCorrection)
export(clusterAnnotation)
export(clusterPropagation)
export(clustering)
export(clustering_with_masking)
export(downsampleSCE)
export(plotClusterHeatmap)
export(plotDR)
export(prepSCE)
export(runUMAP)
export(updateMetadataSCE)
import(ComplexHeatmap)
import(SingleCellExperiment)
import(ggplot2)
importFrom(ConsensusClusterPlus,ConsensusClusterPlus)
importFrom(FlowSOM,BuildSOM)
importFrom(FlowSOM,ReadInput)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(caret,train)
importFrom(caret,trainControl)
importFrom(cydar,dnaGate)
importFrom(cydar,outlierGate)
importFrom(cydar,poolCells)
importFrom(data.table,":=")
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,rbindlist)
importFrom(data.table,setcolorder)
importFrom(dplyr,"%>%")
importFrom(dplyr,bind_rows)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_all)
importFrom(dplyr,n)
importFrom(dplyr,sample_n)
importFrom(dplyr,summarize)
importFrom(dplyr,tally)
importFrom(dplyr,transmute)
importFrom(flowCore,"colnames<-")
importFrom(flowCore,"exprs<-")
importFrom(flowCore,Subset)
importFrom(flowCore,biexponentialTransform)
importFrom(flowCore,colnames)
importFrom(flowCore,estimateLogicle)
importFrom(flowCore,exprs)
importFrom(flowCore,flowFrame)
importFrom(flowCore,fsApply)
importFrom(flowCore,keyword)
importFrom(flowCore,transform)
importFrom(flowCore,transformList)
importFrom(ggedit,remove_geom)
importFrom(ggpubr,compare_means)
importFrom(ggrastr,geom_point_rast)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grid,gpar)
importFrom(harmony,HarmonyMatrix)
importFrom(igraph,cluster_louvain)
importFrom(janitor,make_clean_names)
importFrom(magrittr,set_colnames)
importFrom(magrittr,set_names)
importFrom(magrittr,set_rownames)
importFrom(matrixStats,colQuantiles)
importFrom(matrixStats,rowMedians)
importFrom(matrixStats,rowQuantiles)
importFrom(methods,is)
importFrom(ncdfFlow,as.flowSet)
importFrom(ncdfFlow,read.ncdfFlowSet)
importFrom(parallel,detectCores)
importFrom(purrr,is_empty)
importFrom(purrr,map)
importFrom(purrr,map_depth)
importFrom(scater,plotReducedDim)
importFrom(scran,buildSNNGraph)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,predict)
importFrom(stats,setNames)
importFrom(stringr,str_detect)
importFrom(tidyr,complete)
importFrom(uwot,umap)
importFrom(viridis,scale_color_viridis)
importFrom(viridis,scale_colour_viridis)
importFrom(viridis,scale_fill_viridis)