# Generated by roxygen2: do not edit by hand

export(RNAattributes)
export(RNAdf2se)
export(RNAdicercall)
export(RNAdifferentialAnalysis)
export(RNAdistribution)
export(RNAfeatures)
export(RNAimport)
export(RNAmergeAnnotations)
export(RNAmergeGenomes)
export(RNAmobile)
export(RNApopulation)
export(RNAreorder)
export(RNAsequences)
export(RNAsubset)
export(RNAsummary)
export(mapRNA)
export(plotHeatmap)
export(plotRNAfeatures)
export(plotSampleDistance)
export(plotSamplePCA)
importFrom(BiocGenerics,grep)
importFrom(Biostrings,
  readDNAStringSet,
  writeXStringSet
)
importFrom(DESeq2,
  DESeq,
  DESeqDataSetFromMatrix,
  estimateSizeFactors,
  plotPCA,
  results,
  rlog
)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomicRanges,
  GRanges,
  GRangesList,
  findOverlaps,
  makeGRangesFromDataFrame,
  mcols,
  promoters,
  reduce,
  seqnames
)
importFrom(IRanges,
  IRanges,
  overlapsAny,
  ranges
)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,
  DataFrame,
  elementMetadata,
  mcols,
  queryHits,
  subjectHits
)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(bioseq,
  rna,
  seq_consensus
)
importFrom(data.table,
  ":=",
  data.table,
  fread,
  melt,
  setDT,
  setnames
)
importFrom(dplyr,
  "%>%",
  across,
  case_when,
  contains,
  count,
  filter,
  if_any,
  inner_join,
  mutate,
  mutate_at,
  rename,
  select,
  select_if,
  starts_with,
  where
)
importFrom(edgeR,
  DGEList,
  calcNormFactors,
  estimateDisp,
  exactTest
)
importFrom(ggplot2,
  aes,
  coord_fixed,
  element_blank,
  element_line,
  element_rect,
  element_text,
  expansion,
  facet_wrap,
  geom_bar,
  geom_line,
  geom_point,
  ggplot,
  guide_legend,
  guides,
  labs,
  margin,
  scale_color_manual,
  scale_colour_manual,
  scale_fill_manual,
  theme,
  theme_classic,
  unit,
  xlab,
  ylab
)
importFrom(ggrepel,
  geom_label_repel,
  geom_text_repel
)
importFrom(grDevices,colorRampPalette)
importFrom(grid,
  gpar,
  unit
)
importFrom(pheatmap,pheatmap)
importFrom(progress,progress_bar)
importFrom(reticulate,use_condaenv)
importFrom(rlang,sym)
importFrom(rtracklayer,
  export,
  import,
  import.gff
)
importFrom(scales,label_percent)
importFrom(stats,
  complete.cases,
  dist,
  na.omit,
  p.adjust,
  relevel,
  setNames
)
importFrom(tidyr,
  gather,
  replace_na
)
importFrom(tidyselect,
  all_of,
  starts_with
)
importFrom(utils,
  flush.console,
  read.table,
  write.table
)
