# Generated by roxygen2: do not edit by hand

export(calculatePvalue)
export(exportMBbed)
export(exportMBtable)
export(findSupportingRemapPeaks)
export(motifbreakR)
export(plotMB)
export(shiny_motifbreakR)
export(snps.from.file)
export(snps.from.rsid)
export(variants.from.file)
import(BiocGenerics)
import(BiocParallel)
import(GenomeInfoDb)
import(GenomicRanges)
import(IRanges)
import(S4Vectors)
import(bsicons)
import(bslib)
import(grDevices)
import(methods)
import(shiny)
importClassesFrom(MotifDb,MotifList)
importClassesFrom(motifStack,marker)
importClassesFrom(motifStack,pfm)
importFrom(BSgenome,
  available.genomes,
  snplocs,
  snpsById,
  snpsByOverlaps
)
importFrom(BiocFileCache,
  BiocFileCache,
  bfcadd,
  bfcdownload,
  bfcneedsupdate,
  bfcnew,
  bfcquery,
  bfcrpath
)
importFrom(BiocParallel,
  bplapply,
  bpnworkers
)
importFrom(Biostrings,
  BStringSetList,
  DNAString,
  DNAStringSet,
  DNAStringSetList,
  DNA_ALPHABET,
  IUPAC_CODE_MAP,
  complement,
  getSeq,
  letterFrequency,
  matchPattern,
  replaceAt,
  replaceLetterAt,
  reverseComplement,
  subseq,
  uniqueLetters
)
importFrom(DT,
  DTOutput,
  JS,
  datatable,
  formatRound,
  renderDT
)
importFrom(Gviz,
  AnnotationTrack,
  GenomeAxisTrack,
  HighlightTrack,
  IdeogramTrack,
  SequenceTrack,
  plotTracks
)
importFrom(SummarizedExperiment,rowRanges)
importFrom(TFMPvalue,
  TFMpv2sc,
  TFMsc2pv
)
importFrom(VariantAnnotation,
  ScanVcfParam,
  VcfFile,
  alt,
  isSNV,
  readVcf,
  ref
)
importFrom(biomaRt,
  getBM,
  searchDatasets,
  useEnsembl
)
importFrom(grid,
  gpar,
  grid.newpage,
  popViewport,
  pushViewport,
  viewport
)
importFrom(matrixStats,
  colAlls,
  colMaxs,
  colMins,
  colRanges
)
importFrom(motifStack,
  DNAmotifAlignment,
  addBlank,
  colorset,
  motifStack,
  plotMotifLogo,
  plotMotifLogoStack
)
importFrom(pwalign,
  deletion,
  insertion,
  pairwiseAlignment
)
importFrom(rtracklayer,
  export.bed,
  import
)
importFrom(stringr,
  str_extract,
  str_length,
  str_locate_all,
  str_pad,
  str_remove,
  str_sort,
  str_split,
  str_sub,
  str_trim
)
importFrom(tools,R_user_dir)
importFrom(utils,
  write.csv,
  write.table
)
importFrom(vroom,vroom)
