# Generated by roxygen2: do not edit by hand

export(calcBaseline)
export(calcExpectedMutations)
export(calcObservedMutations)
export(calcTargetingDistance)
export(calculateMutability)
export(collapseClones)
export(consensusSequence)
export(convertNumbering)
export(createBaseline)
export(createMutabilityMatrix)
export(createMutationDefinition)
export(createRegionDefinition)
export(createSubstitutionMatrix)
export(createTargetingMatrix)
export(createTargetingModel)
export(distToNearest)
export(editBaseline)
export(expectedMutations)
export(extendMutabilityMatrix)
export(extendSubstitutionMatrix)
export(findThreshold)
export(groupBaseline)
export(makeAverage1merMut)
export(makeAverage1merSub)
export(makeDegenerate5merMut)
export(makeDegenerate5merSub)
export(makeGraphDf)
export(minNumMutationsTune)
export(minNumSeqMutationsTune)
export(observedMutations)
export(plotBaselineDensity)
export(plotBaselineSummary)
export(plotDensityThreshold)
export(plotGmmThreshold)
export(plotMutability)
export(plotSlideWindowTune)
export(plotTune)
export(setRegionBoundaries)
export(shmulateSeq)
export(shmulateTree)
export(slideWindowDb)
export(slideWindowSeq)
export(slideWindowTune)
export(slideWindowTunePlot)
export(summarizeBaseline)
export(testBaseline)
export(writeTargetingDistance)
exportClasses(Baseline)
exportClasses(DensityThreshold)
exportClasses(GmmThreshold)
exportClasses(MutabilityModel)
exportClasses(MutationDefinition)
exportClasses(RegionDefinition)
exportClasses(TargetingMatrix)
exportClasses(TargetingModel)
exportMethods(as.data.frame)
exportMethods(plot)
exportMethods(print)
exportMethods(summary)
import(ggplot2)
import(graphics)
import(methods)
import(utils)
importFrom(KernSmooth,bkde)
importFrom(MASS,fitdistr)
importFrom(alakazam,
  IUPAC_DNA,
  baseTheme,
  buildPhylipLineage,
  checkColumns,
  cpuCount,
  getAAMatrix,
  getAllele,
  getDNAMatrix,
  getFamily,
  getGene,
  getLocus,
  getMRCA,
  getPathLengths,
  getSegment,
  gridPlot,
  groupGenes,
  isValidAASeq,
  makeChangeoClone,
  nonsquareDist,
  pairwiseDist,
  pairwiseEqual,
  progressBar,
  seqDist,
  seqEqual,
  summarizeSubtrees,
  tableEdges,
  translateStrings
)
importFrom(ape,mst)
importFrom(diptest,dip.test)
importFrom(doParallel,registerDoParallel)
importFrom(dplyr,
  "%>%",
  arrange,
  bind_cols,
  bind_rows,
  combine,
  desc,
  do,
  filter,
  group_by,
  group_indices,
  left_join,
  mutate,
  mutate_at,
  n,
  pull,
  recode,
  rename,
  select,
  summarize,
  summarize_at,
  transmute,
  ungroup
)
importFrom(foreach,
  "%dopar%",
  foreach,
  registerDoSEQ
)
importFrom(igraph,
  "V<-",
  E,
  V,
  as_adjacency_matrix,
  graph_from_data_frame,
  layout_as_tree,
  set_vertex_attr,
  vertex_attr
)
importFrom(iterators,icount)
importFrom(lazyeval,interp)
importFrom(progress,progress_bar)
importFrom(rlang,
  .data,
  sym,
  syms
)
importFrom(scales,
  log10_trans,
  log2_trans,
  math_format,
  percent,
  pretty_breaks,
  scientific,
  trans_breaks,
  trans_format
)
importFrom(seqinr,
  c2s,
  s2c,
  translate,
  words
)
importFrom(stats,
  approx,
  as.dist,
  convolve,
  cor,
  cov,
  cutree,
  dbeta,
  dgamma,
  dnorm,
  ecdf,
  integrate,
  mad,
  median,
  na.exclude,
  na.omit,
  optim,
  optimize,
  p.adjust,
  pbeta,
  pgamma,
  pnorm,
  qbeta,
  rbeta,
  rbinom,
  runif,
  sd,
  setNames,
  uniroot,
  weighted.mean
)
importFrom(stringi,
  stri_count_boundaries,
  stri_count_regex,
  stri_detect_regex,
  stri_dup,
  stri_extract_all_regex,
  stri_extract_first_regex,
  stri_flatten,
  stri_join,
  stri_length,
  stri_replace_all_regex,
  stri_replace_first_regex,
  stri_sub,
  stri_sub_replace
)
importFrom(tidyr,
  gather,
  pivot_wider,
  spread
)
importFrom(tidyselect,
  all_of,
  any_of
)
