# Generated by roxygen2: do not edit by hand

export(ABBREV_AA)
export(DNA_COLORS)
export(DNA_IUPAC)
export(IG_COLORS)
export(IMGT_REGIONS)
export(IUPAC_AA)
export(IUPAC_DNA)
export(TR_COLORS)
export(aliphatic)
export(alphaDiversity)
export(aminoAcidProperties)
export(baseTheme)
export(buildPhylipLineage)
export(bulk)
export(calcCoverage)
export(calcDiversity)
export(charge)
export(checkColumns)
export(collapseDuplicates)
export(combineIgphyml)
export(countClones)
export(countGenes)
export(countPatterns)
export(cpuCount)
export(estimateAbundance)
export(extractVRegion)
export(fastDist)
export(fastDistAA)
export(getAAMatrix)
export(getAllele)
export(getChain)
export(getDNAMatrix)
export(getFamily)
export(getGene)
export(getLocus)
export(getMRCA)
export(getPathLengths)
export(getPositionQuality)
export(getSegment)
export(graphToPhylo)
export(gravy)
export(gridPlot)
export(groupGenes)
export(isValidAASeq)
export(junctionAlignment)
export(makeChangeoClone)
export(makeTempDir)
export(maskPositionsByQuality)
export(maskSeqEnds)
export(maskSeqGaps)
export(nonsquareDist)
export(padSeqEnds)
export(pairwiseDist)
export(pairwiseEqual)
export(permuteLabels)
export(phyloToGraph)
export(plotAbundanceCurve)
export(plotDiversityCurve)
export(plotDiversityTest)
export(plotEdgeTest)
export(plotMRCATest)
export(plotSubtrees)
export(polar)
export(progressBar)
export(rarefyDiversity)
export(readChangeoDb)
export(readFastqDb)
export(readIgphyml)
export(seqDist)
export(seqEqual)
export(seqMismatchCount)
export(seqMismatchMatrix)
export(seqMismatchPositions)
export(sortGenes)
export(stoufferMeta)
export(summarizeSubtrees)
export(tableEdges)
export(testDiversity)
export(testEdges)
export(testMRCA)
export(translateDNA)
export(translateStrings)
export(writeChangeoDb)
exportClasses(AbundanceCurve)
exportClasses(ChangeoClone)
exportClasses(DiversityCurve)
exportClasses(EdgeTest)
exportClasses(MRCATest)
exportMethods(plot)
exportMethods(print)
import(ggplot2)
import(graphics)
import(methods)
import(utils)
importFrom(Biostrings,
  BString,
  extractAt
)
importFrom(GenomicAlignments,
  explodeCigarOpLengths,
  explodeCigarOps
)
importFrom(IRanges,IRanges)
importFrom(Matrix,
  rowSums,
  sparseMatrix
)
importFrom(Rcpp,evalCpp)
importFrom(airr,
  read_rearrangement,
  write_rearrangement
)
importFrom(ape,
  di2multi,
  ladderize,
  read.fastq,
  read.tree,
  reorder.phylo,
  root
)
importFrom(dplyr,
  "%>%",
  all_of,
  arrange,
  bind_cols,
  bind_rows,
  combine,
  desc,
  do,
  filter,
  group_by,
  left_join,
  mutate,
  mutate_at,
  n,
  one_of,
  rename,
  right_join,
  rowwise,
  select,
  slice,
  summarize,
  summarize_at,
  transmute,
  ungroup
)
importFrom(igraph,
  E,
  V,
  all_shortest_paths,
  as_data_frame,
  as_edgelist,
  components,
  degree,
  distances,
  graph_from_adjacency_matrix,
  graph_from_data_frame,
  groups,
  make_directed_graph,
  make_graph,
  make_undirected_graph,
  set_vertex_attr,
  shortest_paths,
  vertex_attr
)
importFrom(progress,progress_bar)
importFrom(readr,
  cols,
  read_delim,
  read_tsv,
  write_delim,
  write_tsv
)
importFrom(rlang,
  ":=",
  enquo,
  sym,
  syms
)
importFrom(scales,
  log10_trans,
  log2_trans,
  math_format,
  percent,
  pretty_breaks,
  scientific,
  trans_breaks,
  trans_format
)
importFrom(seqinr,
  s2c,
  translate
)
importFrom(stats,
  cor,
  cov,
  dbinom,
  dmultinom,
  dnorm,
  ecdf,
  mad,
  median,
  na.omit,
  pbinom,
  pnorm,
  qbinom,
  qnorm,
  rbinom,
  rmultinom,
  rnorm,
  sd,
  setNames
)
importFrom(stringi,
  stri_count_boundaries,
  stri_count_fixed,
  stri_count_regex,
  stri_detect_fixed,
  stri_dup,
  stri_extract_all_regex,
  stri_extract_first_regex,
  stri_flatten,
  stri_join,
  stri_length,
  stri_pad_left,
  stri_pad_right,
  stri_paste,
  stri_replace_all_regex,
  stri_replace_first_regex,
  stri_split_fixed
)
importFrom(tibble,tibble)
importFrom(tidyr,
  complete,
  gather
)
useDynLib(alakazam, .registration=TRUE)
