# Generated by roxygen2: do not edit by hand

export(abundanceVDJ)
export(addVDJtoSCE)
export(barVDJ)
export(boxVDJ)
export(calculateDiversity)
export(clonoAbundance)
export(clonoAssignment)
export(clonoFrequency)
export(clonoGroup)
export(clonoNames)
export(clonoStats)
export(pieVDJ)
export(readVDJcontigs)
export(runBreakaway)
export(runVDJPCA)
export(scatterVDJ)
export(splitClonotypes)
export(summarizeClonotypes)
export(writeVDJcontigs)
exportClasses(clonoStats)
exportMethods(abundanceVDJ)
exportMethods(addVDJtoSCE)
exportMethods(barVDJ)
exportMethods(boxVDJ)
exportMethods(calculateDiversity)
exportMethods(clonoAbundance)
exportMethods(clonoAssignment)
exportMethods(clonoFrequency)
exportMethods(clonoGroup)
exportMethods(clonoNames)
exportMethods(clonoStats)
exportMethods(pieVDJ)
exportMethods(readVDJcontigs)
exportMethods(runBreakaway)
exportMethods(runVDJPCA)
exportMethods(scatterVDJ)
exportMethods(show)
exportMethods(splitClonotypes)
exportMethods(summarizeClonotypes)
exportMethods(writeVDJcontigs)
import(Matrix)
import(Rcpp)
import(methods)
importClassesFrom(IRanges,SplitDataFrameList)
importClassesFrom(Matrix,sparseMatrix)
importClassesFrom(S4Vectors,DataFrame)
importClassesFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
importFrom(IRanges,commonColnames)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,"%in%")
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,coolcat)
importFrom(S4Vectors,match)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,split)
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,colData)
importFrom(cowplot,panel_border)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_polar)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_jitter)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_void)
importFrom(gridExtra,grid.arrange)
importFrom(stats,prcomp)
importFrom(stats,qnorm)
importFrom(utils,read.csv)
importFrom(utils,write.csv)
useDynLib(VDJdive, .registration = TRUE)
