# Generated by roxygen2: do not edit by hand

export("relabundance<-")
export(IdTaxaToDataFrame)
export(ZTransform)
export(addAbundanceClass)
export(addAlpha)
export(addCCA)
export(addCluster)
export(addContaminantQC)
export(addDPCoA)
export(addDissimilarity)
export(addDivergence)
export(addDominant)
export(addHierarchyTree)
export(addJointRPCA)
export(addLDA)
export(addMDS)
export(addMediation)
export(addNMDS)
export(addNMF)
export(addNotContaminantQC)
export(addPerSampleDominantFeatures)
export(addPerSampleDominantTaxa)
export(addPrevalence)
export(addPrevalentAbundance)
export(addRDA)
export(addRPCA)
export(addTaxonomyTree)
export(agglomerateByModule)
export(agglomerateByPrevalence)
export(agglomerateByRank)
export(agglomerateByRanks)
export(agglomerateByVariable)
export(applyByModule)
export(bestDMNFit)
export(calculateCCA)
export(calculateDMN)
export(calculateDMNgroup)
export(calculateDPCoA)
export(calculateJSD)
export(calculateNMDS)
export(calculateOverlap)
export(calculateRDA)
export(calculateUnifrac)
export(checkTaxonomy)
export(cluster)
export(convertFromBIOM)
export(convertFromDADA2)
export(convertFromPhyloseq)
export(convertToBIOM)
export(convertToMAE)
export(convertToPhyloseq)
export(convertToTreeSE)
export(countDominantFeatures)
export(countDominantTaxa)
export(estimateDivergence)
export(estimateDiversity)
export(estimateDominance)
export(estimateEvenness)
export(estimateFaith)
export(estimateRichness)
export(filterRPCAInput)
export(full_join)
export(getAbundanceClass)
export(getAbundant)
export(getAlpha)
export(getBestDMNFit)
export(getCCA)
export(getCluster)
export(getConditionallyLowAbundant)
export(getCrossAssociation)
export(getDMN)
export(getDPCoA)
export(getDissimilarity)
export(getDivergence)
export(getDominant)
export(getExperimentCrossAssociation)
export(getExperimentCrossCorrelation)
export(getHierarchyTree)
export(getJointRPCA)
export(getLDA)
export(getLowAbundant)
export(getMDS)
export(getMediation)
export(getNMDS)
export(getNMF)
export(getPermanentlyLowAbundant)
export(getPrevalence)
export(getPrevalentAbundance)
export(getPrevalentFeatures)
export(getPrevalentTaxa)
export(getRDA)
export(getRPCA)
export(getRare)
export(getRareFeatures)
export(getRareTaxa)
export(getReducedDimAttribute)
export(getTaxonomyLabels)
export(getTaxonomyRanks)
export(getTop)
export(getTopFeatures)
export(getTopTaxa)
export(getUnique)
export(getUniqueFeatures)
export(getUniqueTaxa)
export(importBIOM)
export(importHUMAnN)
export(importMetaPhlAn)
export(importMothur)
export(importQIIME2)
export(importQZA)
export(importTaxpasta)
export(inner_join)
export(left_join)
export(loadFromBiom)
export(loadFromHumann)
export(loadFromMetaphlan)
export(loadFromMothur)
export(loadFromQIIME2)
export(makePhyloseqFromTreeSE)
export(makePhyloseqFromTreeSummarizedExperiment)
export(makeTreeSEFromBiom)
export(makeTreeSEFromDADA2)
export(makeTreeSEFromPhyloseq)
export(makeTreeSummarizedExperimentFromBiom)
export(makeTreeSummarizedExperimentFromDADA2)
export(makeTreeSummarizedExperimentFromPhyloseq)
export(mapTaxonomy)
export(meltAssay)
export(meltSE)
export(mergeCols)
export(mergeFeatures)
export(mergeFeaturesByPrevalence)
export(mergeFeaturesByRank)
export(mergeRows)
export(mergeSEs)
export(mergeSamples)
export(perSampleDominantFeatures)
export(perSampleDominantTaxa)
export(performDMNgroupCV)
export(plotNMDS)
export(rarefyAssay)
export(readQZA)
export(relAbundanceCounts)
export(relabundance)
export(right_join)
export(runCCA)
export(runDMN)
export(runDPCoA)
export(runJSD)
export(runNMDS)
export(runOverlap)
export(runRDA)
export(runUnifrac)
export(setTaxonomyRanks)
export(splitByRanks)
export(splitOn)
export(subsampleCounts)
export(subsetByPrevalent)
export(subsetByPrevalentFeatures)
export(subsetByPrevalentTaxa)
export(subsetByRare)
export(subsetByRareFeatures)
export(subsetByRareTaxa)
export(subsetFeatures)
export(subsetSamples)
export(subsetTaxa)
export(summarizeDominance)
export(summary)
export(taxonomyRankEmpty)
export(taxonomyRanks)
export(taxonomyTree)
export(testExperimentCrossAssociation)
export(testExperimentCrossCorrelation)
export(transformAssay)
export(transformCounts)
export(transformFeatures)
export(transformSamples)
export(unsplitByRanks)
export(unsplitOn)
exportMethods("relabundance<-")
exportMethods(ZTransform)
exportMethods(addAbundanceClass)
exportMethods(addAlpha)
exportMethods(addCCA)
exportMethods(addCluster)
exportMethods(addContaminantQC)
exportMethods(addDissimilarity)
exportMethods(addDivergence)
exportMethods(addDominant)
exportMethods(addHierarchyTree)
exportMethods(addJointRPCA)
exportMethods(addLDA)
exportMethods(addMDS)
exportMethods(addMediation)
exportMethods(addNMF)
exportMethods(addNotContaminantQC)
exportMethods(addPERMANOVA)
exportMethods(addPerSampleDominantFeatures)
exportMethods(addPerSampleDominantTaxa)
exportMethods(addPrevalence)
exportMethods(addPrevalentAbundance)
exportMethods(addRDA)
exportMethods(addRPCA)
exportMethods(addTaxonomyTree)
exportMethods(agglomerateByModule)
exportMethods(agglomerateByPrevalence)
exportMethods(agglomerateByRank)
exportMethods(agglomerateByRanks)
exportMethods(agglomerateByVariable)
exportMethods(applyByModule)
exportMethods(bestDMNFit)
exportMethods(calculateDMN)
exportMethods(calculateDMNgroup)
exportMethods(calculateJSD)
exportMethods(calculateOverlap)
exportMethods(calculateUnifrac)
exportMethods(checkTaxonomy)
exportMethods(cluster)
exportMethods(convertToBIOM)
exportMethods(convertToMAE)
exportMethods(convertToPhyloseq)
exportMethods(convertToTreeSE)
exportMethods(countDominantFeatures)
exportMethods(countDominantTaxa)
exportMethods(estimateDivergence)
exportMethods(estimateDiversity)
exportMethods(estimateDominance)
exportMethods(estimateEvenness)
exportMethods(estimateFaith)
exportMethods(estimateRichness)
exportMethods(filterRPCAInput)
exportMethods(full_join)
exportMethods(getAbundanceClass)
exportMethods(getAbundant)
exportMethods(getAlpha)
exportMethods(getBestDMNFit)
exportMethods(getCCA)
exportMethods(getCluster)
exportMethods(getConditionallyLowAbundant)
exportMethods(getCrossAssociation)
exportMethods(getDMN)
exportMethods(getDPCoA)
exportMethods(getDissimilarity)
exportMethods(getDivergence)
exportMethods(getDominant)
exportMethods(getExperimentCrossAssociation)
exportMethods(getExperimentCrossCorrelation)
exportMethods(getHierarchyTree)
exportMethods(getJointRPCA)
exportMethods(getLDA)
exportMethods(getLowAbundant)
exportMethods(getMDS)
exportMethods(getMediation)
exportMethods(getNMDS)
exportMethods(getNMF)
exportMethods(getPERMANOVA)
exportMethods(getPermanentlyLowAbundant)
exportMethods(getPrevalence)
exportMethods(getPrevalent)
exportMethods(getPrevalentAbundance)
exportMethods(getPrevalentFeatures)
exportMethods(getPrevalentTaxa)
exportMethods(getRDA)
exportMethods(getRPCA)
exportMethods(getRare)
exportMethods(getRareFeatures)
exportMethods(getRareTaxa)
exportMethods(getReducedDimAttribute)
exportMethods(getTaxonomyLabels)
exportMethods(getTop)
exportMethods(getTopFeatures)
exportMethods(getTopTaxa)
exportMethods(getUnique)
exportMethods(getUniqueFeatures)
exportMethods(getUniqueTaxa)
exportMethods(inner_join)
exportMethods(isContaminant)
exportMethods(isNotContaminant)
exportMethods(left_join)
exportMethods(makePhyloseqFromTreeSE)
exportMethods(makePhyloseqFromTreeSummarizedExperiment)
exportMethods(makeTreeSummarizedExperimentFromPhyloseq)
exportMethods(mapTaxonomy)
exportMethods(meltAssay)
exportMethods(meltSE)
exportMethods(mergeCols)
exportMethods(mergeFeatures)
exportMethods(mergeFeaturesByPrevalence)
exportMethods(mergeFeaturesByRank)
exportMethods(mergeRows)
exportMethods(mergeSEs)
exportMethods(mergeSamples)
exportMethods(perSampleDominantFeatures)
exportMethods(perSampleDominantTaxa)
exportMethods(performDMNgroupCV)
exportMethods(rarefyAssay)
exportMethods(relAbundanceCounts)
exportMethods(relabundance)
exportMethods(right_join)
exportMethods(runJSD)
exportMethods(runOverlap)
exportMethods(splitOn)
exportMethods(subsampleCounts)
exportMethods(subsetByPrevalent)
exportMethods(subsetByPrevalentFeatures)
exportMethods(subsetByPrevalentTaxa)
exportMethods(subsetByRare)
exportMethods(subsetByRareFeatures)
exportMethods(subsetByRareTaxa)
exportMethods(subsetFeatures)
exportMethods(subsetSamples)
exportMethods(subsetTaxa)
exportMethods(summarizeDominance)
exportMethods(summary)
exportMethods(taxonomyRankEmpty)
exportMethods(taxonomyRanks)
exportMethods(taxonomyTree)
exportMethods(testExperimentCrossAssociation)
exportMethods(testExperimentCrossCorrelation)
exportMethods(transformAssay)
exportMethods(transformFeatures)
exportMethods(transformSamples)
exportMethods(unsplitByRanks)
exportMethods(unsplitOn)
import(DelayedArray)
import(TreeSummarizedExperiment)
import(methods)
import(scater)
importFrom(BiocGenerics,
  "%in%",
  cbind,
  grepl,
  rbind
)
importFrom(BiocParallel,
  SerialParam,
  bpisup,
  bplapply,
  bpmapply,
  bpparam,
  bpstart,
  bpstop,
  register
)
importFrom(Biostrings,
  DNAStringSet,
  DNAStringSetList,
  readDNAStringSet
)
importFrom(DECIPHER,ConsensusSequence)
importFrom(DelayedArray,
  DelayedArray,
  colSums,
  getAutoBPPARAM,
  rowSums,
  rowsum,
  setAutoBPPARAM,
  type
)
importFrom(DelayedMatrixStats,
  colQuantiles,
  colSums2,
  rowMaxs,
  rowMeans2,
  rowMedians,
  rowMins,
  rowSums2
)
importFrom(DirichletMultinomial,
  AIC,
  BIC,
  cvdmngroup,
  dmn,
  dmngroup,
  laplace
)
importFrom(IRanges,
  CharacterList,
  IntegerList,
  LogicalList,
  NumericList,
  relist
)
importFrom(MASS,isoMDS)
importFrom(MatrixGenerics,rowSums2)
importFrom(MultiAssayExperiment,
  ExperimentList,
  MultiAssayExperiment,
  experiments,
  intersectColumns,
  sampleMap
)
importFrom(Rcpp,
  evalCpp,
  sourceCpp
)
importFrom(S4Vectors,
  "metadata<-",
  DataFrame,
  SimpleList,
  as.data.frame,
  make_zero_col_DFrame,
  metadata,
  pc,
  splitAsList,
  unfactor
)
importFrom(SingleCellExperiment,
  "altExp<-",
  "altExps<-",
  "reducedDim<-",
  "reducedDims<-",
  SingleCellExperiment,
  altExp,
  altExpNames,
  altExps,
  reducedDim,
  reducedDimNames,
  reducedDims
)
importFrom(SummarizedExperiment,
  "assay<-",
  "assays<-",
  "colData<-",
  "rowData<-",
  SummarizedExperiment,
  assay,
  assayNames,
  assays,
  colData,
  rowData,
  rowRanges
)
importFrom(TreeSummarizedExperiment,
  changeTree,
  subsetByLeaf
)
importFrom(ape,
  as.phylo,
  bind.tree,
  collapse.singles,
  cophenetic.phylo,
  drop.tip,
  has.singles,
  is.binary,
  is.rooted,
  node.depth.edgelength,
  read.tree,
  reorder.phylo
)
importFrom(bluster,clusterRows)
importFrom(decontam,
  isContaminant,
  isNotContaminant
)
importFrom(dplyr,
  "%>%",
  arrange,
  as_tibble,
  bind_cols,
  bind_rows,
  coalesce,
  desc,
  group_by,
  mutate,
  n,
  rename,
  select,
  summarise,
  sym,
  tally
)
importFrom(rlang,
  ":=",
  sym
)
importFrom(scater,calculateMDS)
importFrom(stats,
  TukeyHSD,
  anova,
  as.dist,
  as.formula,
  chisq.test,
  cmdscale,
  cor,
  cor.test,
  dist,
  formula,
  gaussian,
  glm,
  hclust,
  lm,
  median,
  na.fail,
  na.omit,
  p.adjust,
  runif,
  sd,
  setNames,
  terms
)
importFrom(stringr,
  str_extract,
  str_extract_all,
  str_pad,
  str_replace_all
)
importFrom(tibble,
  rownames_to_column,
  tibble
)
importFrom(tidyr,
  as_tibble,
  ends_with,
  pivot_longer,
  pivot_wider,
  starts_with,
  unnest,
  unnest_wider
)
importFrom(utils,
  assignInMyNamespace,
  combn,
  getFromNamespace,
  head,
  read.delim,
  read.table,
  unzip
)
importFrom(vegan,
  "sppscores<-",
  adonis2,
  anova.cca,
  avgdist,
  betadisper,
  cca,
  dbrda,
  decostand,
  eigenvals,
  monoMDS,
  optspace,
  permutest,
  rrarefy,
  scores,
  vegdist
)
useDynLib(mia)
useDynLib(mia, .registration = TRUE)
