# Generated by roxygen2: do not edit by hand

S3method("[[",Pi)
S3method("[[",PiCellPropData)
S3method("[[",PiDSData)
S3method("[[",PiData)
S3method("[[",PiDataList)
S3method("[[",PiExpFreqData)
S3method("[[",PiMarkerData)
S3method("[[",PiParentMetaData)
S3method("[[<-",Pi)
S3method(AddPiData,Pi)
S3method(AddPiData,PiData)
S3method(AddPiData,PiDataList)
S3method(AddPiData,default)
S3method(CheckPiData,Pi)
S3method(CheckPiData,PiCellPropData)
S3method(CheckPiData,PiDSData)
S3method(CheckPiData,PiDataList)
S3method(CheckPiData,PiExpFreqData)
S3method(CheckPiData,PiMarkerData)
S3method(CheckPiData,PiParentMetaData)
S3method(CheckPiData,default)
S3method(print,Pi)
S3method(print,PiCellPropData)
S3method(print,PiDSData)
S3method(print,PiData)
S3method(print,PiDataList)
S3method(print,PiExpFreqData)
S3method(print,PiMarkerData)
S3method(print,PiParentMetaData)
export(AddPiData)
export(CalculateExpFreqs)
export(CheckPiData)
export(ConfigureReprojection)
export(CreatePostIntegrationObject)
export(ExportPiData)
export(Pi)
export(PiCellPropData)
export(PiDSData)
export(PiData)
export(PiDataList)
export(PiExpFreqData)
export(PiMarkerData)
export(PiParentMetaData)
export(RunAnnotatedDotPlot)
export(RunDSDotPlot)
export(RunDimPlot)
export(RunExpressionPlot)
export(RunFindAllMarkers)
export(RunMatrixPlot)
export(RunProportionPlot)
export(RunPseudobulkAnalysis)
export(RunSankeyPlot)
export(RunStackedVlnPlot)
export(RunSummarizedHeatmap)
export(SankeyPlot)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,anno_text)
importFrom(Matrix,rowSums)
importFrom(SingleCellExperiment,colData)
importFrom(SingleCellExperiment,counts)
importFrom(aplot,xlim2)
importFrom(circlize,colorRamp2)
importFrom(cowplot,get_legend)
importFrom(cowplot,plot_grid)
importFrom(cowplot,theme_nothing)
importFrom(crayon,blue)
importFrom(crayon,bold)
importFrom(crayon,cyan)
importFrom(crayon,green)
importFrom(crayon,magenta)
importFrom(crayon,red)
importFrom(crayon,yellow)
importFrom(dplyr,"%>%")
importFrom(dplyr,group_by)
importFrom(dplyr,n)
importFrom(dplyr,summarise)
importFrom(dplyr,summarize)
importFrom(future,nbrOfWorkers)
importFrom(future,plan)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expansion)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_errorbar)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_jitter)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,position_jitterdodge)
importFrom(ggplot2,position_nudge)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_continuous)
importFrom(ggplot2,scale_fill_gradient2)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,vars)
importFrom(ggprism,add_pvalue)
importFrom(ggsankey,geom_sankey)
importFrom(ggsankey,geom_sankey_text)
importFrom(ggsankey,make_long)
importFrom(ggsankey,theme_sankey)
importFrom(ggtree,ggtree)
importFrom(ggtree,layout_dendrogram)
importFrom(gplots,colorpanel)
importFrom(grid,gpar)
importFrom(grid,unit)
importFrom(limma,makeContrasts)
importFrom(muscat,aggregateData)
importFrom(muscat,pbDS)
importFrom(muscat,prepSCE)
importFrom(muscat,resDS)
importFrom(patchwork,plot_layout)
importFrom(patchwork,plot_spacer)
importFrom(randomcoloR,distinctColorPalette)
importFrom(reshape2,dcast)
importFrom(reshape2,melt)
importFrom(rstatix,add_significance)
importFrom(rstatix,add_x_position)
importFrom(rstatix,add_y_position)
importFrom(rstatix,drop_na)
importFrom(rstatix,group_by)
importFrom(scales,hue_pal)
importFrom(scales,squish)
importFrom(uwot,umap)
