NAMESPACE

# Generated by roxygen2: do not edit by hand

export(StartracDiversity)
export(abundanceContig)
export(addVariable)
export(alluvialClonotypes)
export(clonalDiversity)
export(clonalHomeostasis)
export(clonalNetwork)
export(clonalOverlap)
export(clonalOverlay)
export(clonalProportion)
export(clonesizeDistribution)
export(clonotypeBias)
export(clusterTCR)
export(combineBCR)
export(combineExpression)
export(combineTCR)
export(combineTRUST4)
export(compareClonotypes)
export(createHTOContigList)
export(expression2List)
export(getCirclize)
export(highlightClonotypes)
export(lengthContig)
export(loadContigs)
export(occupiedscRepertoire)
export(quantContig)
export(scatterClonotype)
export(stripBarcode)
export(subsetContig)
export(vizGenes)
exportClasses(StartracOut)
import(dplyr)
import(ggplot2)
importFrom(SeuratObject,Embeddings)
importFrom(SeuratObject,Idents)
importFrom(SingleCellExperiment,colData)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,colData)
importFrom(doParallel,registerDoParallel)
importFrom(dplyr,"%>%")
importFrom(dplyr,bind_rows)
importFrom(dplyr,count)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,sample_n)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,summarize_all)
importFrom(ggalluvial,StatStratum)
importFrom(ggalluvial,geom_alluvium)
importFrom(ggalluvial,geom_flow)
importFrom(ggalluvial,geom_stratum)
importFrom(ggalluvial,to_lodes_form)
importFrom(ggplot2,ggplot)
importFrom(ggraph,circle)
importFrom(ggraph,geom_edge_bend)
importFrom(ggraph,geom_node_point)
importFrom(ggraph,ggraph)
importFrom(ggraph,guide_edge_colourbar)
importFrom(ggraph,scale_edge_colour_gradientn)
importFrom(igraph,V)
importFrom(igraph,`V<-`)
importFrom(igraph,components)
importFrom(igraph,graph_from_data_frame)
importFrom(methods,"slot<-")
importFrom(methods,new)
importFrom(methods,slot)
importFrom(methods,validObject)
importFrom(parallel,detectCores)
importFrom(parallel,makeCluster)
importFrom(parallel,stopCluster)
importFrom(plyr,adply)
importFrom(plyr,join)
importFrom(plyr,laply)
importFrom(plyr,ldply)
importFrom(plyr,llply)
importFrom(powerTCR,fdiscgammagpd)
importFrom(powerTCR,get_distances)
importFrom(reshape2,dcast)
importFrom(reshape2,melt)
importFrom(rlang,"%||%")
importFrom(stats,na.omit)
importFrom(stats,sd)
importFrom(stringdist,stringdistmatrix)
importFrom(stringr,str_c)
importFrom(stringr,str_replace_na)
importFrom(stringr,str_sort)
importFrom(stringr,str_split)
importFrom(tidygraph,activate)
importFrom(tidygraph,as_tbl_graph)
importFrom(utils,combn)
importFrom(utils,head)
importFrom(vegan,diversity)
importFrom(vegan,estimateR)