# Generated by roxygen2: do not edit by hand

export(cleanVariants)
export(digestSalmon)
export(genomogrify)
export(indelcator)
export(overdispFromBoots)
export(overlapsByVar)
export(owl)
export(parY)
export(shiftByVar)
export(sjFromExons)
export(transmogrify)
export(upsetVarByCol)
export(varTags)
export(varTypes)
exportMethods(cleanVariants)
exportMethods(genomogrify)
exportMethods(indelcator)
exportMethods(overlapsByVar)
exportMethods(owl)
exportMethods(transmogrify)
import(Biostrings)
import(GenomicRanges)
importClassesFrom(BSgenome,BSgenome)
importClassesFrom(SummarizedExperiment,SummarizedExperiment)
importClassesFrom(VariantAnnotation,ScanVcfParam)
importClassesFrom(VariantAnnotation,VcfFile)
importFrom(BSgenome,getSeq)
importFrom(Biostrings,
  IUPAC_CODE_MAP,
  getSeq
)
importFrom(GenomicFeatures,extractTranscriptSeqs)
importFrom(IRanges,
  "width<-",
  IRanges,
  Views,
  end,
  findOverlaps,
  overlapsAny,
  start,
  subsetByOverlaps,
  width
)
importFrom(S4Vectors,
  "mcols<-",
  "metadata<-",
  DataFrame,
  Rle,
  mcols,
  queryHits,
  splitAsList,
  subjectHits
)
importFrom(Seqinfo,
  "genome<-",
  "seqinfo<-",
  "seqlengths<-",
  "seqlevels<-",
  seqinfo,
  seqlengths,
  seqlevels,
  seqlevelsInUse,
  seqnames
)
importFrom(SummarizedExperiment,
  SummarizedExperiment,
  rowRanges
)
importFrom(VariantAnnotation,
  "vcfWhich<-",
  ScanVcfParam,
  readVcf
)
importFrom(data.table,fread)
importFrom(ggplot2,
  guide_none,
  guides,
  scale_fill_discrete
)
importFrom(matrixStats,
  rowMeans2,
  rowSums2,
  rowVars
)
importFrom(methods,
  as,
  is,
  slot
)
importFrom(parallel,mclapply)
importFrom(patchwork,plot_annotation)
importFrom(stats,
  aggregate,
  as.formula,
  median,
  qf,
  setNames
)
useDynLib(transmogR, .registration = TRUE)
