# Generated by roxygen2: do not edit by hand

S3method(is.nan,data.frame)
export("assay<-")
export("assayNames<-")
export("assays<-")
export("colData<-")
export("rowData<-")
export(ASEFilter)
export(ASE_DESeq)
export(ASE_DoubleExpSeq)
export(ASE_edgeR)
export(ASE_edgeR_timeseries)
export(ASE_limma)
export(ASE_limma_timeseries)
export(BAM2COV)
export(STAR_alignExperiment)
export(STAR_alignReads)
export(STAR_buildGenome)
export(STAR_buildRef)
export(STAR_loadGenomeGTF)
export(STAR_mappability)
export(STAR_version)
export(SpliceWiz_example_NxtSE)
export(SpliceWiz_example_bams)
export(addPSI_edgeR)
export(applyFilters)
export(assay)
export(assayNames)
export(assays)
export(buildFullRef)
export(buildRef)
export(calculateMappability)
export(colData)
export(collateData)
export(coord2GR)
export(extract_gene_ids_for_GO)
export(findBAMS)
export(findFASTQ)
export(findSamples)
export(findSpliceWizOutput)
export(fitASE_edgeR)
export(fitASE_edgeR_custom)
export(generateSyntheticReads)
export(getAvailableGO)
export(getCoverage)
export(getCoverageBins)
export(getCoverageData)
export(getCoverageRegions)
export(getCoverage_DF)
export(getDefaultFilters)
export(getGenomeData)
export(getNonPolyARef)
export(getPlotObject)
export(getResources)
export(goASE)
export(goGenes)
export(isCOV)
export(makeMatrix)
export(makeMeanPSI)
export(makeSE)
export(plotAnnoTrack)
export(plotCoverage)
export(plotGO)
export(plotGenome)
export(plotView)
export(processBAM)
export(rowData)
export(runFilter)
export(setSWthreads)
export(spliceWiz)
export(subset_EventNames_by_GO)
export(testASE_edgeR)
export(theme_white)
export(theme_white_legend)
export(theme_white_legend_plot_track)
export(viewASE)
export(viewExons)
export(viewGO)
export(viewGenes)
export(viewIR)
export(viewIR_NMD)
export(viewIntrons)
export(viewProteins)
export(viewTranscripts)
exportClasses(ASEFilter)
exportClasses(NxtSE)
exportClasses(covDataObject)
exportClasses(covPlotObject)
exportClasses(covPlotly)
exportMethods("[")
exportMethods("[<-")
exportMethods("covfile<-")
exportMethods("down_exc<-")
exportMethods("down_inc<-")
exportMethods("sampleQC<-")
exportMethods("up_exc<-")
exportMethods("up_inc<-")
exportMethods(cbind)
exportMethods(coerce)
exportMethods(condition)
exportMethods(covfile)
exportMethods(down_exc)
exportMethods(down_inc)
exportMethods(getExonRanges)
exportMethods(junc_PSI)
exportMethods(junc_counts)
exportMethods(junc_counts_uns)
exportMethods(junc_gr)
exportMethods(rbind)
exportMethods(realize_NxtSE)
exportMethods(ref)
exportMethods(row_gr)
exportMethods(sampleQC)
exportMethods(setResolution)
exportMethods(showEvents)
exportMethods(showExons)
exportMethods(sourcePath)
exportMethods(tracks)
exportMethods(up_exc)
exportMethods(up_inc)
exportMethods(update_NxtSE)
import(NxtIRFdata)
import(data.table)
import(ggplot2)
import(ompBAM)
import(shiny)
import(shinydashboard)
importClassesFrom(S4Vectors,DataFrame)
importClassesFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(AnnotationHub,
  AnnotationHub,
  cache,
  query,
  removeResources
)
importFrom(BSgenome,getSeq)
importFrom(BiocFileCache,
  BiocFileCache,
  bfcquery,
  bfcrpath
)
importFrom(BiocGenerics,
  "end<-",
  "start<-",
  cbind,
  end,
  ncol,
  nrow,
  rbind,
  start,
  width
)
importFrom(BiocParallel,
  MulticoreParam,
  SerialParam,
  SnowParam,
  bplapply,
  bpparam
)
importFrom(Biostrings,
  DNAStringSet,
  readDNAStringSet,
  translate
)
importFrom(DT,
  dataTableProxy,
  datatable,
  selectRows
)
importFrom(DelayedArray,
  DelayedArray,
  plogis,
  qlogis,
  rowMeans,
  rowSums
)
importFrom(DelayedMatrixStats,
  rowAnyNAs,
  rowMaxs,
  rowSds
)
importFrom(GenomeInfoDb,
  "seqinfo<-",
  "seqlevels<-",
  "seqlevelsStyle<-",
  genomeStyles,
  seqinfo,
  seqlengths,
  seqlevels,
  seqlevelsStyle,
  sortSeqlevels
)
importFrom(GenomicRanges,
  "seqnames<-",
  "strand<-",
  GRanges,
  disjoin,
  findOverlaps,
  flank,
  makeGRangesFromDataFrame,
  makeGRangesListFromDataFrame,
  psetdiff,
  reduce,
  seqnames,
  setdiff,
  split,
  strand
)
importFrom(HDF5Array,
  HDF5Array,
  writeHDF5Array
)
importFrom(IRanges,
  IRanges,
  RleList,
  Views
)
importFrom(R.utils,gzip)
importFrom(RColorBrewer,brewer.pal.info)
importFrom(RSQLite,SQLite)
importFrom(Rcpp,evalCpp)
importFrom(S4Vectors,
  "mcols<-",
  "metadata<-",
  DataFrame,
  Rle,
  SimpleList,
  bindCOLS,
  bindROWS,
  from,
  getListElement,
  mcols,
  metadata,
  setListElement,
  setValidity2,
  to
)
importFrom(SummarizedExperiment,
  "assay<-",
  "assayNames<-",
  "assays<-",
  "colData<-",
  "rowData<-",
  SummarizedExperiment,
  assay,
  assayNames,
  assays,
  colData,
  rowData
)
importFrom(fst,
  read.fst,
  threads_fst,
  write.fst
)
importFrom(genefilter,rowttests)
importFrom(grDevices,colorRampPalette)
importFrom(h5mread,h5writeDimnames)
importFrom(heatmaply,heatmaply)
importFrom(htmltools,
  singleton,
  tagList
)
importFrom(httr,
  GET,
  timeout
)
importFrom(magrittr,"%>%")
importFrom(matrixStats,colVars)
importFrom(methods,
  as,
  callNextMethod,
  coerce,
  is,
  new,
  show,
  validObject
)
importFrom(parallel,detectCores)
importFrom(patchwork,
  area,
  plot_layout,
  wrap_plots
)
importFrom(pheatmap,pheatmap)
importFrom(plotly,
  add_ribbons,
  add_trace,
  config,
  event_data,
  event_register,
  event_unregister,
  ggplotly,
  highlight,
  layout,
  orca,
  partial_bundle,
  plot_ly,
  plotlyOutput,
  plotlyProxy,
  plotlyProxyInvoke,
  plotly_build,
  renderPlotly,
  subplot,
  toWebGL
)
importFrom(progress,progress_bar)
importFrom(rhandsontable,
  hot_col,
  hot_to_r,
  rHandsontableOutput,
  renderRHandsontable,
  rhandsontable
)
importFrom(rhdf5,
  h5createDataset,
  h5createFile,
  h5createGroup,
  h5delete,
  h5write
)
importFrom(rtracklayer,
  TwoBitFile,
  export,
  import,
  track
)
importFrom(rvest,
  html_attr,
  html_nodes,
  read_html
)
importFrom(scales,
  cut_si,
  label_number
)
importFrom(shinyFiles,
  getVolumes,
  parseDirPath,
  parseFilePaths,
  parseSavePath,
  shinyDirButton,
  shinyDirChoose,
  shinyFileChoose,
  shinyFileSave,
  shinyFilesButton,
  shinySaveButton
)
importFrom(shinyWidgets,
  actionBttn,
  ask_confirmation,
  materialSwitch,
  prettyRadioButtons,
  radioGroupButtons,
  sendSweetAlert,
  sliderTextInput,
  switchInput,
  updateRadioGroupButtons,
  updateSliderTextInput,
  updateSwitchInput
)
importFrom(stats,
  aggregate,
  as.formula,
  complete.cases,
  model.matrix,
  na.omit,
  p.adjust,
  prcomp,
  qt,
  runif
)
importFrom(stringi,stri_locate_first_fixed)
importFrom(tools,R_user_dir)
importFrom(utils,
  download.file,
  getFromNamespace,
  head,
  packageVersion,
  setTxtProgressBar,
  txtProgressBar
)
useDynLib(SpliceWiz, .registration = TRUE)
