# Generated by roxygen2: do not edit by hand

export(addRankDivisionPlot)
export(calcPresSpec)
export(checkColorPalette)
export(checkIdNewtaxa)
export(checkInputValidity)
export(checkNewick)
export(checkOmaID)
export(clusterDataDend)
export(compareMedianTaxonGroups)
export(compareTaxonGroups)
export(createArchiPlot)
export(createDimRedPlotData)
export(createGeneAgePlot)
export(createLongMatrix)
export(createPercentageDistributionData)
export(createProfileFromOma)
export(createUnrootedTree)
export(createVarDistPlot)
export(createVariableDistributionData)
export(createVariableDistributionDataSubset)
export(dataCustomizedPlot)
export(dataFeatureTaxGroup)
export(dataMainPlot)
export(dataVarDistTaxGroup)
export(dimReduction)
export(estimateGeneAge)
export(fastaParser)
export(featureDistTaxPlot)
export(filterProfileData)
export(fromInputToProfile)
export(geneAgePlotDf)
export(generateSinglePlot)
export(getAllDomainsOma)
export(getAllFastaOma)
export(getCommonAncestor)
export(getCoreGene)
export(getDataClustering)
export(getDataForOneOma)
export(getDendrogram)
export(getDistanceMatrix)
export(getFastaFromFasInput)
export(getFastaFromFile)
export(getFastaFromFolder)
export(getIDsRank)
export(getInputTaxaID)
export(getInputTaxaName)
export(getNameList)
export(getOmaDataForOneOrtholog)
export(getOmaDomainFromURL)
export(getOmaMembers)
export(getQualColForVector)
export(getSelectedFastaOma)
export(getSelectedTaxonNames)
export(getTaxonomyInfo)
export(getTaxonomyMatrix)
export(getTaxonomyRanks)
export(gridArrangeSharedLegend)
export(groupLabelDimRedData)
export(heatmapPlotting)
export(heatmapPlottingFast)
export(highlightProfilePlot)
export(id2name)
export(linearizeArchitecture)
export(mainTaxonomyRank)
export(parseDomainInput)
export(parseInfoProfile)
export(plotDimRed)
export(plotDimRed3D)
export(prepareDimRedData)
export(processNcbiTaxonomy)
export(processOrthoID)
export(reduceProfile)
export(runPhyloProfile)
export(sortInputTaxa)
export(sortTaxaFromTree)
export(taxonomyTableCreator)
export(varDistTaxPlot)
export(wideToLong)
export(xmlParser)
import(BiocStyle)
import(bit64, except = c(setdiff, intersect, union, setequal))
import(bsplus)
import(data.table, except = c(first, last, between))
import(dplyr)
import(ggplot2)
import(plotly, except = c(last_plot, select))
import(scattermore)
import(svglite)
import(tsne)
import(umap)
importFrom(Biostrings,readAAStringSet)
importFrom(DT,
  dataTableOutput,
  renderDataTable
)
importFrom(RColorBrewer,
  brewer.pal,
  brewer.pal.info
)
importFrom(RCurl,url.exists)
importFrom(ape,
  as.phylo,
  plot.phylo,
  read.tree,
  root
)
importFrom(bioDist,
  cor.dist,
  mutualInfo
)
importFrom(colourpicker,colourInput)
importFrom(data.table,
  dcast,
  fread,
  melt,
  rbindlist,
  setDT,
  setnames,
  transpose
)
importFrom(dplyr,
  add_count,
  arrange,
  count,
  distinct,
  filter,
  group_by,
  inner_join,
  left_join,
  mutate,
  select,
  summarise,
  tibble
)
importFrom(energy,dcor)
importFrom(fastcluster,hclust)
importFrom(grDevices,colorRampPalette)
importFrom(grid,
  convertHeight,
  grobHeight,
  unit
)
importFrom(gridExtra,
  arrangeGrob,
  grid.arrange
)
importFrom(htmlwidgets,saveWidget)
importFrom(pbapply,pblapply)
importFrom(shinyFiles,
  parseDirPath,
  shinyDirButton,
  shinyDirChoose
)
importFrom(shinycssloaders,withSpinner)
importFrom(shinyjs,
  disable,
  enable,
  html,
  reset,
  toggleState
)
importFrom(stats,
  aggregate,
  as.dist,
  complete.cases,
  dist,
  na.omit
)
importFrom(stringr,
  str_count,
  str_split_fixed,
  str_wrap
)
importFrom(utils,
  head,
  tail
)
importFrom(xml2,
  read_xml,
  xml_attr,
  xml_find_all
)
importFrom(yaml,
  read_yaml,
  write_yaml
)
importFrom(zoo,na.locf)
