# Generated by roxygen2: do not edit by hand

export(APPconf)
export(availableThemes)
export(createAppConfig)
export(createDataSet)
export(extractFragmentNameMapList)
export(scInit)
export(scRNAseqApp)
exportClasses(APPconf)
exportMethods("$")
exportMethods("$<-")
exportMethods("[")
exportMethods("[[")
exportMethods("[[<-")
exportMethods(as.character)
exportMethods(as.list)
exportMethods(lapply)
exportMethods(markers)
exportMethods(show)
exportMethods(unlist)
import(shiny)
importFrom(ComplexHeatmap,
  Heatmap,
  HeatmapAnnotation,
  Legend,
  draw,
  merge_dendrogram,
  pindex,
  rowAnnotation
)
importFrom(DBI,
  dbAppendTable,
  dbClearResult,
  dbConnect,
  dbDisconnect,
  dbExecute,
  dbExistsTable,
  dbGetQuery,
  dbListFields,
  dbListTables,
  dbReadTable,
  dbSendQuery,
  dbWithTransaction,
  dbWriteTable,
  sqlInterpolate
)
importFrom(DT,
  DTOutput,
  JS,
  dataTableProxy,
  datatable,
  formatRound,
  renderDT,
  replaceData
)
importFrom(GenomeInfoDb,
  "seqinfo<-",
  "seqlevelsStyle<-",
  keepSeqlevels,
  seqinfo,
  seqlengths,
  seqlevels,
  seqlevelsStyle,
  seqnames
)
importFrom(GenomicRanges,
  "end<-",
  "start<-",
  "strand<-",
  GRanges,
  GRangesList,
  coverage,
  end,
  gaps,
  makeGRangesFromDataFrame,
  reduce,
  seqnames,
  start,
  strand,
  tileGenome,
  width
)
importFrom(IRanges,
  IRanges,
  Views,
  nearest,
  ranges,
  shift,
  subsetByOverlaps,
  tile,
  viewMeans
)
importFrom(Matrix,sparseMatrix)
importFrom(RColorBrewer,
  brewer.pal,
  brewer.pal.info
)
importFrom(RSQLite,SQLite)
importFrom(RefManageR,
  GetBibEntryWithDOI,
  GetPubMedByID,
  PrintBibliography
)
importFrom(Rsamtools,
  TabixFile,
  scanTabix,
  seqnamesTabix
)
importFrom(S4Vectors,
  DataFrame,
  SimpleList,
  mcols,
  split
)
importFrom(Seurat,
  CellCycleScoring,
  CreateSeuratObject,
  FindAllMarkers,
  FindVariableFeatures,
  Read10X,
  ScaleData,
  as.SingleCellExperiment
)
importFrom(SeuratObject,
  "DefaultAssay<-",
  "Idents<-",
  "Misc<-",
  Assays,
  CreateDimReducObject,
  DefaultAssay,
  DefaultBoundary,
  DefaultFOV,
  Embeddings,
  GetAssayData,
  GetTissueCoordinates,
  Idents,
  Images,
  Misc,
  Molecules,
  Reductions,
  VariableFeatures
)
importFrom(SingleCellExperiment,reducedDim)
importFrom(bibtex,read.bib)
importFrom(bslib,
  bs_current_theme,
  bs_get_variables,
  bs_theme,
  bs_themer,
  input_dark_mode,
  nav_item,
  nav_spacer
)
importFrom(circlize,colorRamp2)
importFrom(colourpicker,colourInput)
importFrom(data.table,
  ":=",
  .I,
  .N,
  .SD,
  as.data.table,
  data.table,
  dcast.data.table,
  fread,
  rbindlist,
  setDT,
  setnames,
  setorderv,
  uniqueN
)
importFrom(desc,
  desc,
  desc_get_maintainer
)
importFrom(fs,path_sanitize)
importFrom(ggdendro,dendro_data)
importFrom(ggforce,
  geom_arc_bar,
  geom_bezier,
  geom_circle,
  geom_mark_hull
)
importFrom(ggnewscale,new_scale_fill)
importFrom(ggplot2,
  .data,
  GeomPolygon,
  GeomViolin,
  aes,
  after_stat,
  annotate,
  coord_cartesian,
  coord_equal,
  coord_fixed,
  coord_flip,
  element_blank,
  element_line,
  element_rect,
  element_text,
  facet_grid,
  geom_bar,
  geom_boxplot,
  geom_col,
  geom_density_2d,
  geom_density_2d_filled,
  geom_hline,
  geom_jitter,
  geom_line,
  geom_point,
  geom_polygon,
  geom_raster,
  geom_rect,
  geom_ribbon,
  geom_segment,
  geom_smooth,
  geom_text,
  geom_tile,
  geom_violin,
  ggplot,
  ggplot_build,
  ggplot_gtable,
  ggproto,
  ggsave,
  guide_colorbar,
  guide_legend,
  guides,
  labs,
  layer,
  layer_scales,
  position_dodge,
  scale_color_gradient2,
  scale_color_gradientn,
  scale_color_manual,
  scale_colour_identity,
  scale_colour_manual,
  scale_fill_gradient,
  scale_fill_gradientn,
  scale_fill_identity,
  scale_fill_manual,
  scale_x_continuous,
  scale_y_continuous,
  scale_y_discrete,
  theme,
  theme_classic,
  theme_minimal,
  unit,
  vars,
  xlab,
  xlim,
  ylab,
  ylim
)
importFrom(ggrepel,geom_text_repel)
importFrom(ggridges,
  geom_density_ridges,
  theme_ridges
)
importFrom(grDevices,
  col2rgb,
  colorRampPalette,
  dev.off,
  hcl.colors,
  pdf,
  pdfFonts,
  rgb
)
importFrom(grid,
  arrow,
  convertWidth,
  current.viewport,
  gpar,
  grid.circle,
  grid.lines,
  grid.xaxis,
  grid.yaxis,
  grobName,
  grobTree,
  seekViewport,
  unit,
  unit.c
)
importFrom(gridExtra,
  arrangeGrob,
  grid.arrange
)
importFrom(htmltools,
  htmlDependency,
  singleton,
  tagList,
  tags
)
importFrom(jsonlite,
  fromJSON,
  parse_json
)
importFrom(magrittr,"%>%")
importFrom(markdown,markdownToHTML)
importFrom(methods,
  `slot<-`,
  as,
  getPackageName,
  is,
  new,
  prototype,
  representation,
  setAs,
  setClass,
  setClassUnion,
  setMethod,
  show,
  slot,
  slotNames
)
importFrom(patchwork,wrap_plots)
importFrom(plotly,
  event_data,
  event_register,
  ggplotly,
  layout,
  plot_ly,
  plotlyOutput,
  renderPlotly,
  toWebGL
)
importFrom(promises,
  "%...!%",
  "%...>%",
  future_promise
)
importFrom(reshape2,melt)
importFrom(rhdf5,
  H5Fclose,
  H5Fopen,
  H5Lexists,
  h5closeAll,
  h5createDataset,
  h5createFile,
  h5createGroup,
  h5ls,
  h5read,
  h5readAttributes,
  h5write,
  h5writeAttribute
)
importFrom(rtracklayer,
  export,
  import
)
importFrom(scales,
  rescale,
  zero_range
)
importFrom(scrypt,hashPassword)
importFrom(shiny,
  NS,
  Progress,
  actionButton,
  column,
  downloadHandler,
  fluidRow,
  getDefaultReactiveDomain,
  icon,
  markdown
)
importFrom(shinyhelper,
  helper,
  observe_helpers
)
importFrom(shinymanager,
  auth_ui,
  check_credentials,
  create_db,
  fab_button,
  pwd_ui,
  read_db_decrypt,
  secure_app,
  secure_server,
  use_language,
  write_db_encrypt
)
importFrom(slingshot,
  SlingshotDataSet,
  getLineages,
  slingClusterLabels,
  slingLineages,
  slingMST,
  slingParams
)
importFrom(sortable,rank_list)
importFrom(stats,
  as.dendrogram,
  as.formula,
  chisq.test,
  cor,
  dist,
  hclust,
  loess,
  phyper,
  prcomp,
  predict,
  quantile,
  rnorm,
  setNames,
  weighted.mean,
  wilcox.test
)
importFrom(tools,file_ext)
importFrom(utils,
  adist,
  bibentry,
  combn,
  download.file,
  getFromNamespace,
  globalVariables,
  head,
  packageDescription,
  packageVersion,
  read.csv,
  read.delim,
  read.table,
  write.csv,
  write.table
)
importFrom(xfun,
  base64_uri,
  is_abs_path
)
importFrom(xml2,
  as_list,
  read_xml
)
importMethodsFrom(BiocGenerics,lapply)
importMethodsFrom(Matrix,summary)
