# Generated by roxygen2: do not edit by hand

export("geneSets<-")
export("gsvaAnnotation<-")
export(avgParam)
export(computeGeneSetsOverlap)
export(deduplicateGeneSets)
export(filterGeneSets)
export(geneIdsToGeneSetCollection)
export(geneSetSizes)
export(geneSets)
export(gsva)
export(gsvaAnnotation)
export(gsvaBatchtoolsSlurmParam)
export(gsvaColRanks)
export(gsvaColScores)
export(gsvaEnrichment)
export(gsvaMap)
export(gsvaParam)
export(gsvaRanks)
export(gsvaReduce)
export(gsvaRowNorm)
export(gsvaScores)
export(guessGeneIdType)
export(igsva)
export(loadHDF5GSVA)
export(loadHDF5GSVAranks)
export(plageParam)
export(readGMT)
export(saveHDF5GSVA)
export(saveHDF5GSVAranks)
export(spatCor)
export(ssgseaParam)
export(zscoreParam)
exportClasses(GsvaExprData)
exportClasses(GsvaGeneSets)
exportClasses(GsvaMethodParam)
exportClasses(avgParam)
exportClasses(gsvaParam)
exportClasses(gsvaRanksParam)
exportClasses(plageParam)
exportClasses(ssgseaParam)
exportClasses(zscoreParam)
exportMethods(computeGeneSetsOverlap)
exportMethods(details)
exportMethods(filterGeneSets)
exportMethods(geneSetSizes)
exportMethods(geneSets)
exportMethods(gsva)
exportMethods(gsvaAnnotation)
exportMethods(gsvaRanks)
exportMethods(gsvaScores)
exportMethods(spatCor)
import(methods)
importClassesFrom(Biobase,ExpressionSet)
importClassesFrom(DelayedArray,DelayedArray)
importClassesFrom(DelayedArray,DelayedMatrix)
importClassesFrom(GSEABase,GeneIdentifierType)
importClassesFrom(GSEABase,GeneSet)
importClassesFrom(GSEABase,GeneSetCollection)
importClassesFrom(HDF5Array,HDF5Array)
importClassesFrom(HDF5Array,HDF5Matrix)
importClassesFrom(IRanges,IRanges)
importClassesFrom(Matrix,dgCMatrix)
importClassesFrom(SingleCellExperiment,SingleCellExperiment)
importClassesFrom(SparseArray,SVT_SparseMatrix)
importClassesFrom(SpatialExperiment,SpatialExperiment)
importClassesFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(Biobase,selectSome)
importFrom(BiocGenerics,
  "annotation<-",
  "type<-",
  annotation,
  cbind,
  rbind,
  sort,
  type
)
importFrom(BiocParallel,
  "bpprogressbar<-",
  "bpstopOnError<-",
  BatchtoolsParam,
  MulticoreParam,
  SerialParam,
  SnowParam,
  batchtoolsRegistryargs,
  bplapply,
  bpnworkers,
  bpok,
  bpprogressbar,
  bptry
)
importFrom(DelayedArray,
  blockApply,
  blockReduce,
  chunkGrid,
  chunkdim,
  close,
  colAutoGrid,
  defaultAutoGrid,
  getAutoBlockLength,
  gridReduce,
  rowAutoGrid,
  rowRanges,
  seed,
  setAutoBPPARAM
)
importFrom(DelayedMatrixStats,rowSds)
importFrom(GSEABase,
  AnnoOrEntrezIdentifier,
  ENSEMBLIdentifier,
  EntrezIdentifier,
  NullCollection,
  NullIdentifier,
  SymbolIdentifier,
  details,
  geneIdType,
  geneIds,
  mapIdentifiers
)
importFrom(HDF5Array,
  HDF5RealizationSink,
  loadHDF5SummarizedExperiment,
  saveHDF5SummarizedExperiment,
  writeHDF5Array
)
importFrom(IRanges,
  CharacterList,
  IRanges,
  IntegerList,
  end,
  match,
  ranges,
  start,
  width
)
importFrom(Matrix,nnzero)
importFrom(MatrixGenerics,
  colMeans,
  colRanks,
  colSums,
  rowMeans,
  rowSds,
  rowSums
)
importFrom(S4Arrays,
  ArrayViewport,
  DummyArrayGrid,
  is_sparse,
  read_block,
  refdim,
  write_block
)
importFrom(S4Vectors,
  "metadata<-",
  DataFrame,
  SimpleList,
  metadata
)
importFrom(SingleCellExperiment,
  SingleCellExperiment,
  altExps,
  reducedDims
)
importFrom(SparseArray,
  NaArray,
  SparseArray,
  is_nonna,
  nzcount,
  rowMeans,
  rowSds
)
importFrom(SpatialExperiment,SpatialExperiment)
importFrom(SummarizedExperiment,
  "assay<-",
  SummarizedExperiment,
  assay,
  assayNames
)
importFrom(cli,
  cli_abort,
  cli_alert_danger,
  cli_alert_info,
  cli_alert_success,
  cli_alert_warning,
  cli_progress_bar,
  cli_progress_done,
  cli_progress_update
)
importFrom(graphics,
  abline,
  grid,
  lines,
  plot,
  segments
)
importFrom(memuse,
  Sys.meminfo,
  howbig
)
importFrom(methods,
  callNextMethod,
  getClass,
  is,
  isClass,
  new
)
importFrom(sparseMatrixStats,
  colRanks,
  rowRanges
)
importFrom(stats,
  dist,
  ecdf,
  na.omit,
  pnorm,
  rnorm,
  rpois,
  sd
)
importFrom(utils,
  capture.output,
  globalVariables,
  head,
  installed.packages,
  packageDescription,
  tail
)
importMethodsFrom(Biobase,experimentData)
importMethodsFrom(Biobase,exprs)
importMethodsFrom(Biobase,featureNames)
importMethodsFrom(Biobase,phenoData)
importMethodsFrom(BiocParallel,"bpprogressbar<-")
importMethodsFrom(BiocParallel,bplapply)
importMethodsFrom(GSEABase,GeneSet)
importMethodsFrom(GSEABase,GeneSetCollection)
importMethodsFrom(GSEABase,geneIds)
importMethodsFrom(GSEABase,incidence)
importMethodsFrom(S4Vectors,"metadata<-")
importMethodsFrom(S4Vectors,metadata)
importMethodsFrom(SpatialExperiment,imgData)
importMethodsFrom(SpatialExperiment,spatialCoords)
importMethodsFrom(SummarizedExperiment,assayNames)
importMethodsFrom(SummarizedExperiment,assays)
importMethodsFrom(SummarizedExperiment,colData)
importMethodsFrom(SummarizedExperiment,rowData)
useDynLib(GSVA, .registration=TRUE)
