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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method("DefaultAssayVDJ<-",Seurat)
S3method("DefaultChainVDJ<-",Seurat)
S3method(DefaultAssayVDJ,Seurat)
S3method(DefaultChainVDJ,Seurat)
export("DefaultAssayVDJ<-")
export("DefaultChainVDJ<-")
export(BarplotChainRegion)
export(BarplotClonotypes)
export(CDR3Plot)
export(CircosPlotChains)
export(CircosPlotGenes)
export(CloneConnGraph)
export(ClonotypeDiversity)
export(ClonotypeFrequency)
export(ColorThemes)
export(DefaultAssayVDJ)
export(DefaultChainVDJ)
export(DefineClonotypes)
export(DimplotChainRegion)
export(ExpansionPlot)
export(FeaturePlotClonotype)
export(GetCategoricalColorPalette)
export(GetSequence)
export(HeatmapChainRegion)
export(Interactive_DALI)
export(IsValidSeuratObject)
export(LineageTree)
export(MergeVDJ)
export(PlotSHM)
export(Read10X_AIRR)
export(Read10X_multi_vdj)
export(Read10X_vdj)
export(Read_AIRR)
export(SplitObject_VDJ)
export(SubsetObject_VDJ)
export(TrajectoryPlot)
export(VDJDoublets)
export(VolcanoPlotDEG)
importFrom(Polychrome,sky.colors)
importFrom(Seurat,AddMetaData)
importFrom(Seurat,FeaturePlot)
importFrom(Seurat,FindClusters)
importFrom(Seurat,FindNeighbors)
importFrom(Seurat,SplitObject)
importFrom(circlize,CELL_META)
importFrom(circlize,chordDiagram)
importFrom(circlize,circos.text)
importFrom(circlize,circos.track)
importFrom(dplyr,"%>%")
importFrom(dplyr,add_count)
importFrom(dplyr,all_of)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,count)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,first)
importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(dplyr,group_map)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_if)
importFrom(dplyr,n)
importFrom(dplyr,na_if)
importFrom(dplyr,pull)
importFrom(dplyr,rename_all)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,ungroup)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_jitter)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,labs)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,scale_color_discrete)
importFrom(ggplot2,scale_color_gradient2)
importFrom(ggplot2,scale_color_gradientn)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_colour_gradient2)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(ggraph,geom_edge_arc)
importFrom(ggraph,geom_node_point)
importFrom(ggraph,ggraph)
importFrom(ggraph,scale_edge_alpha)
importFrom(ggraph,scale_edge_color_manual)
importFrom(ggraph,scale_edge_width)
importFrom(ggrepel,geom_text_repel)
importFrom(ggridges,geom_density_ridges)
importFrom(ggridges,theme_ridges)
importFrom(ggtree,geom_tiplab)
importFrom(ggtree,geom_tippoint)
importFrom(ggtree,ggtree)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,hcl)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,strwidth)
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,slot)
importFrom(reshape2,melt)
importFrom(rlang,.data)
importFrom(scales,muted)
importFrom(slingshot,slingshot)
importFrom(stats,na.omit)
importFrom(stringr,str_match)
importFrom(stringr,str_replace_all)
importFrom(tibble,column_to_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tidygraph,as_tbl_graph)
importFrom(tidyr,spread)
importFrom(treeio,full_join)
importFrom(utils,installed.packages)
importFrom(utils,read.csv)