# 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,
  bplapply
)
importFrom(IRanges,commonColnames)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,
  "%in%",
  "metadata<-",
  DataFrame,
  coolcat,
  match,
  metadata,
  split
)
importFrom(SummarizedExperiment,
  "colData<-",
  colData
)
importFrom(cowplot,panel_border)
importFrom(ggplot2,
  aes,
  coord_polar,
  element_blank,
  geom_boxplot,
  geom_col,
  geom_jitter,
  geom_text,
  ggplot,
  labs,
  scale_color_manual,
  scale_fill_continuous,
  theme,
  theme_bw,
  theme_void
)
importFrom(gridExtra,grid.arrange)
importFrom(stats,
  prcomp,
  qnorm
)
importFrom(utils,
  read.csv,
  write.csv
)
useDynLib(VDJdive, .registration = TRUE)
