# Generated by roxygen2: do not edit by hand

export(annoSeqlogo)
export(bin)
export(calcBinnedKmerEnr)
export(calcBinnedMotifEnrHomer)
export(calcBinnedMotifEnrR)
export(dumpJaspar)
export(findHomer)
export(findMotifHits)
export(getColsByBin)
export(getKmerFreq)
export(getZeroBin)
export(homerToPFMatrixList)
export(motifKmerSimilarity)
export(motifSimilarity)
export(parseHomerOutput)
export(plotBinDensity)
export(plotBinDiagnostics)
export(plotBinHist)
export(plotBinScatter)
export(plotMotifHeatmaps)
export(plotSelectionProb)
export(plotStabilityPaths)
export(prepareHomer)
export(randLassoStabSel)
export(sampleRandomRegions)
export(seqLogoGrob)
export(setZeroBin)
importFrom(BSgenome,getSeq)
importFrom(BiocGenerics,
  sort,
  strand,
  width
)
importFrom(BiocParallel,
  SerialParam,
  bplapply,
  bpnworkers
)
importFrom(Biostrings,
  DNAStringSet,
  DNA_ALPHABET,
  DNA_BASES,
  alphabetFrequency,
  fasta.seqlengths,
  matchPWM,
  oligonucleotideFrequency,
  reverseComplement
)
importFrom(ComplexHeatmap,
  AnnotationFunction,
  Heatmap,
  HeatmapAnnotation,
  add_heatmap,
  rowAnnotation,
  subset_gp
)
importFrom(GenomicRanges,
  "end<-",
  GRanges,
  end,
  findOverlaps,
  seqnames,
  sort,
  start,
  strand,
  width
)
importFrom(IRanges,
  IRanges,
  start,
  width
)
importFrom(RSQLite,
  SQLite,
  dbConnect,
  dbDisconnect
)
importFrom(S4Vectors,
  DataFrame,
  Rle,
  isEmpty,
  mcols,
  metadata,
  queryHits,
  split,
  subjectHits
)
importFrom(Seqinfo,
  seqlengths,
  seqlevels,
  seqnames
)
importFrom(SummarizedExperiment,
  SummarizedExperiment,
  assay,
  assayNames,
  colData,
  rowData
)
importFrom(TFBSTools,
  ID,
  Matrix,
  PFMatrix,
  PFMatrixList,
  PWMatrix,
  PWMatrixList,
  getMatrixSet,
  name,
  toPWM
)
importFrom(XVector,subseq)
importFrom(circlize,colorRamp2)
importFrom(cli,
  cli_abort,
  cli_alert_info,
  cli_inform,
  cli_progress_step,
  cli_warn
)
importFrom(ggplot2,
  aes,
  element_blank,
  geom_area,
  geom_col,
  geom_histogram,
  geom_hline,
  geom_line,
  geom_point,
  geom_rug,
  geom_segment,
  geom_text,
  geom_violin,
  ggplot,
  guide_legend,
  guides,
  labs,
  scale_color_manual,
  scale_colour_manual,
  scale_fill_manual,
  scale_x_continuous,
  scale_y_continuous,
  theme,
  theme_classic,
  ylim
)
importFrom(glmnet,glmnet)
importFrom(grDevices,
  col2rgb,
  colorRampPalette
)
importFrom(grid,
  gpar,
  grid.draw,
  grid.rect,
  polygonGrob,
  popViewport,
  pushViewport,
  unit,
  viewport
)
importFrom(methods,
  .valueClassTest,
  as,
  existsMethod,
  formalArgs,
  is,
  show
)
importFrom(rlang,.data)
importFrom(stabs,stabsel)
importFrom(stats,
  cor,
  density,
  dist,
  fisher.test,
  hclust,
  kmeans,
  median,
  model.matrix,
  p.adjust,
  pbinom,
  ppois,
  predict,
  quantile,
  reorder,
  runif
)
importFrom(tidyr,
  pivot_longer,
  starts_with
)
importFrom(tools,file_path_as_absolute)
importFrom(utils,
  getFromNamespace,
  read.delim,
  read.table,
  strcapture,
  write.table
)
