# Generated by roxygen2: do not edit by hand

export(IdTaxaToDataFrame)
export(TAXONOMY_RANKS)
export(ZTransform)
export(addContaminantQC)
export(addNotContaminantQC)
export(addPerSampleDominantFeatures)
export(addPerSampleDominantTaxa)
export(agglomerateByPrevalence)
export(bestDMNFit)
export(calculateDMN)
export(calculateDMNgroup)
export(calculateDPCoA)
export(calculateJSD)
export(calculateNMDS)
export(calculateOverlap)
export(calculateUnifrac)
export(countDominantFeatures)
export(countDominantTaxa)
export(estimateDivergence)
export(estimateDiversity)
export(estimateDominance)
export(estimateEvenness)
export(estimateFaith)
export(estimateRichness)
export(full_join)
export(getAbundanceFeature)
export(getAbundanceSample)
export(getBestDMNFit)
export(getDMN)
export(getExperimentCrossAssociation)
export(getExperimentCrossCorrelation)
export(getPrevalence)
export(getPrevalentAbundance)
export(getPrevalentFeatures)
export(getPrevalentTaxa)
export(getRareFeatures)
export(getRareTaxa)
export(getTopFeatures)
export(getTopTaxa)
export(getUniqueFeatures)
export(getUniqueTaxa)
export(inner_join)
export(left_join)
export(loadFromBiom)
export(loadFromMetaphlan)
export(loadFromMothur)
export(loadFromQIIME2)
export(makePhyloseqFromTreeSE)
export(makePhyloseqFromTreeSummarizedExperiment)
export(makeTreeSEFromBiom)
export(makeTreeSEFromDADA2)
export(makeTreeSEFromPhyloseq)
export(makeTreeSummarizedExperimentFromBiom)
export(makeTreeSummarizedExperimentFromDADA2)
export(makeTreeSummarizedExperimentFromPhyloseq)
export(meltAssay)
export(mergeCols)
export(mergeRows)
export(mergeSEs)
export(perSampleDominantFeatures)
export(perSampleDominantTaxa)
export(performDMNgroupCV)
export(plotNMDS)
export(readQZA)
export(relAbundanceCounts)
export(relabundance)
export(right_join)
export(runDMN)
export(runDPCoA)
export(runJSD)
export(runNMDS)
export(runOverlap)
export(runUnifrac)
export(splitByRanks)
export(splitOn)
export(subsampleCounts)
export(subsetByPrevalentFeatures)
export(subsetByPrevalentTaxa)
export(subsetByRareFeatures)
export(subsetByRareTaxa)
export(subsetFeatures)
export(subsetSamples)
export(subsetTaxa)
export(testExperimentCrossAssociation)
export(testExperimentCrossCorrelation)
export(transformCounts)
export(transformFeatures)
export(transformSamples)
export(unsplitByRanks)
export(unsplitOn)
exportMethods("relabundance<-")
exportMethods(ZTransform)
exportMethods(addContaminantQC)
exportMethods(addNotContaminantQC)
exportMethods(addPerSampleDominantFeatures)
exportMethods(addPerSampleDominantTaxa)
exportMethods(addTaxonomyTree)
exportMethods(agglomerateByPrevalence)
exportMethods(agglomerateByRank)
exportMethods(bestDMNFit)
exportMethods(calculateCCA)
exportMethods(calculateDMN)
exportMethods(calculateDMNgroup)
exportMethods(calculateDPCoA)
exportMethods(calculateJSD)
exportMethods(calculateNMDS)
exportMethods(calculateOverlap)
exportMethods(calculateRDA)
exportMethods(calculateUnifrac)
exportMethods(checkTaxonomy)
exportMethods(countDominantFeatures)
exportMethods(countDominantTaxa)
exportMethods(estimateDivergence)
exportMethods(estimateDiversity)
exportMethods(estimateDominance)
exportMethods(estimateEvenness)
exportMethods(estimateFaith)
exportMethods(estimateRichness)
exportMethods(full_join)
exportMethods(getAbundanceFeature)
exportMethods(getAbundanceSample)
exportMethods(getBestDMNFit)
exportMethods(getDMN)
exportMethods(getExperimentCrossAssociation)
exportMethods(getExperimentCrossCorrelation)
exportMethods(getPrevalence)
exportMethods(getPrevalentAbundance)
exportMethods(getPrevalentFeatures)
exportMethods(getPrevalentTaxa)
exportMethods(getRareFeatures)
exportMethods(getRareTaxa)
exportMethods(getTaxonomyLabels)
exportMethods(getTopFeatures)
exportMethods(getTopTaxa)
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(mergeCols)
exportMethods(mergeRows)
exportMethods(mergeSEs)
exportMethods(perSampleDominantFeatures)
exportMethods(perSampleDominantTaxa)
exportMethods(performDMNgroupCV)
exportMethods(relAbundanceCounts)
exportMethods(relabundance)
exportMethods(right_join)
exportMethods(runCCA)
exportMethods(runOverlap)
exportMethods(runRDA)
exportMethods(splitByRanks)
exportMethods(splitOn)
exportMethods(subsampleCounts)
exportMethods(subsetByPrevalentFeatures)
exportMethods(subsetByPrevalentTaxa)
exportMethods(subsetByRareFeatures)
exportMethods(subsetByRareTaxa)
exportMethods(subsetFeatures)
exportMethods(subsetSamples)
exportMethods(subsetTaxa)
exportMethods(summary)
exportMethods(taxonomyRankEmpty)
exportMethods(taxonomyRanks)
exportMethods(taxonomyTree)
exportMethods(testExperimentCrossAssociation)
exportMethods(testExperimentCrossCorrelation)
exportMethods(transformCounts)
exportMethods(transformFeatures)
exportMethods(transformSamples)
exportMethods(unsplitByRanks)
exportMethods(unsplitOn)
import(DelayedArray)
import(TreeSummarizedExperiment)
import(methods)
import(scater)
importFrom(BiocGenerics,"%in%")
importFrom(BiocGenerics,cbind)
importFrom(BiocGenerics,grepl)
importFrom(BiocGenerics,rbind)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bpisup)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpstart)
importFrom(BiocParallel,bpstop)
importFrom(BiocParallel,register)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,DNAStringSetList)
importFrom(Biostrings,readDNAStringSet)
importFrom(DECIPHER,ConsensusSequence)
importFrom(DelayedArray,DelayedArray)
importFrom(DelayedArray,colSums)
importFrom(DelayedArray,getAutoBPPARAM)
importFrom(DelayedArray,rowSums)
importFrom(DelayedArray,setAutoBPPARAM)
importFrom(DelayedMatrixStats,colMeans2)
importFrom(DelayedMatrixStats,colRanks)
importFrom(DelayedMatrixStats,colSds)
importFrom(DelayedMatrixStats,colSums2)
importFrom(DelayedMatrixStats,rowMaxs)
importFrom(DelayedMatrixStats,rowMeans2)
importFrom(DelayedMatrixStats,rowMedians)
importFrom(DelayedMatrixStats,rowMins)
importFrom(DelayedMatrixStats,rowSums2)
importFrom(DirichletMultinomial,AIC)
importFrom(DirichletMultinomial,BIC)
importFrom(DirichletMultinomial,cvdmngroup)
importFrom(DirichletMultinomial,dmn)
importFrom(DirichletMultinomial,dmngroup)
importFrom(DirichletMultinomial,laplace)
importFrom(IRanges,CharacterList)
importFrom(IRanges,IntegerList)
importFrom(IRanges,LogicalList)
importFrom(IRanges,NumericList)
importFrom(IRanges,relist)
importFrom(MASS,isoMDS)
importFrom(MultiAssayExperiment,ExperimentList)
importFrom(MultiAssayExperiment,MultiAssayExperiment)
importFrom(MultiAssayExperiment,experiments)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,as.data.frame)
importFrom(S4Vectors,make_zero_col_DFrame)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,pc)
importFrom(S4Vectors,splitAsList)
importFrom(S4Vectors,unfactor)
importFrom(SingleCellExperiment,"altExp<-")
importFrom(SingleCellExperiment,"altExps<-")
importFrom(SingleCellExperiment,"reducedDim<-")
importFrom(SingleCellExperiment,"reducedDims<-")
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,altExp)
importFrom(SingleCellExperiment,altExpNames)
importFrom(SingleCellExperiment,altExps)
importFrom(SingleCellExperiment,reducedDims)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(ape,cophenetic.phylo)
importFrom(ape,is.rooted)
importFrom(ape,keep.tip)
importFrom(ape,node.depth)
importFrom(ape,node.depth.edgelength)
importFrom(ape,prop.part)
importFrom(ape,read.tree)
importFrom(ape,reorder.phylo)
importFrom(ape,root)
importFrom(decontam,isContaminant)
importFrom(decontam,isNotContaminant)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,coalesce)
importFrom(dplyr,desc)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,tally)
importFrom(rlang,":=")
importFrom(rlang,sym)
importFrom(scuttle,sumCountsAcrossFeatures)
importFrom(scuttle,summarizeAssayByGroup)
importFrom(stats,as.dist)
importFrom(stats,as.formula)
importFrom(stats,chisq.test)
importFrom(stats,cmdscale)
importFrom(stats,cor)
importFrom(stats,cor.test)
importFrom(stats,hclust)
importFrom(stats,median)
importFrom(stats,p.adjust)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,terms)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(utils,combn)
importFrom(utils,head)
importFrom(utils,read.table)
importFrom(utils,unzip)
importFrom(vegan,monoMDS)
importFrom(vegan,scores)
importFrom(vegan,vegdist)
