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# Generated by roxygen2: do not edit by hand
export(collapseEffectSizeLong)
export(cor.BLAS)
export(directEScombi)
export(directEScombiFromLongTable)
export(effectsize)
export(loginfo)
export(matrix.waterfall)
export(plotDistFromCellInfoTable)
export(plotDotPlotFromGeneTable)
export(plotMatrix.simple)
export(run.cutree)
export(run.cutreeDynamic)
export(simple.removeBatchEffect)
export(ssc.assay.hclust)
export(ssc.assay.zscore)
export(ssc.average.cell)
export(ssc.average.gene)
export(ssc.build)
export(ssc.displayName2id)
export(ssc.downsample)
export(ssc.id2displayName)
export(ssc.moduleScore)
export(ssc.order)
export(ssc.plot.GeneDensity)
export(ssc.plot.cor)
export(ssc.plot.heatmap)
export(ssc.plot.pca)
export(ssc.plot.silhouette)
export(ssc.plot.tsne)
export(ssc.plot.violin)
export(ssc.scale)
export(ssc.toLongTable)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,decorate_annotation)
importFrom(DelayedArray,DelayedArray)
importFrom(DelayedMatrixStats,rowSds)
importFrom(Matrix,colMeans)
importFrom(Matrix,rowMeans)
importFrom(Matrix,t)
importFrom(RColorBrewer,brewer.pal)
importFrom(RColorBrewer,brewer.pal.info)
importFrom(RhpcBLASctl,omp_get_num_procs)
importFrom(RhpcBLASctl,omp_set_num_threads)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,`metadata<-`)
importFrom(S4Vectors,metadata)
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,`reducedDims<-`)
importFrom(SingleCellExperiment,colData)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,reducedDims)
importFrom(SingleCellExperiment,rowData)
importFrom(SummarizedExperiment,`assay<-`)
importFrom(SummarizedExperiment,`colData<-`)
importFrom(SummarizedExperiment,`rowData<-`)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,rowData)
importFrom(circlize,colorRamp2)
importFrom(cluster,silhouette)
importFrom(cowplot,plot_grid)
importFrom(cowplot,save_plot)
importFrom(data.table,`:=`)
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,dcast)
importFrom(data.table,frank)
importFrom(data.table,melt)
importFrom(data.table,setkey)
importFrom(data.table,setorderv)
importFrom(dendextend,color_branches)
importFrom(dendextend,cutree)
importFrom(dendextend,set)
importFrom(doParallel,registerDoParallel)
importFrom(dynamicTreeCut,cutreeDynamic)
importFrom(fields,image.plot)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,cut_number)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expand_limits)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,position_dodge2)
importFrom(ggplot2,scale_colour_brewer)
importFrom(ggplot2,scale_colour_distiller)
importFrom(ggplot2,scale_colour_gradientn)
importFrom(ggplot2,scale_colour_manual)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(ggplot2,scale_size)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggpubr,ggbarplot)
importFrom(ggpubr,ggboxplot)
importFrom(ggpubr,ggscatter)
importFrom(ggpubr,stat_compare_means)
importFrom(ggpubr,stat_cor)
importFrom(ggpubr,theme_pubr)
importFrom(ggrastr,geom_point_rast)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,heat.colors)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(grDevices,rainbow)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,box)
importFrom(graphics,layout)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,plot.new)
importFrom(graphics,points)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(grid,gpar)
importFrom(grid,grid.text)
importFrom(grid,pushViewport)
importFrom(grid,unit)
importFrom(gridBase,baseViewports)
importFrom(ks,kde)
importFrom(limma,lmFit)
importFrom(magrittr,`%>%`)
importFrom(matrixStats,colMedians)
importFrom(moduleColor,plotHclustColors)
importFrom(plyr,laply)
importFrom(plyr,ldply)
importFrom(plyr,llply)
importFrom(scales,viridis_pal)
importFrom(scattermore,geom_scattermore)
importFrom(scattermore,geom_scattermost)
importFrom(stats,as.dendrogram)
importFrom(stats,as.dist)
importFrom(stats,density)
importFrom(stats,dist)
importFrom(stats,fisher.test)
importFrom(stats,hclust)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,order.dendrogram)
importFrom(stats,p.adjust)
importFrom(stats,pnorm)
importFrom(stats,prop.test)
importFrom(stats,quantile)
importFrom(stats,rnorm)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(utils,head)
importFrom(utils,packageVersion)
importFrom(utils,read.table)
importFrom(utils,write.table)