mia-package	mia-package
addAbundanceClass	getAbundant
addAbundanceClass,SingleCellExperiment-method	getAbundant
addAbundanceClass,SummarizedExperiment-method	getAbundant
addAlpha	addAlpha
addAlpha,SummarizedExperiment-method	addAlpha
addCCA	runCCA
addCCA,SingleCellExperiment-method	runCCA
addCluster	addCluster
addCluster,SingleCellExperiment-method	addCluster
addCluster,SummarizedExperiment-method	addCluster
addContaminantQC	isContaminant
addContaminantQC,SummarizedExperiment-method	isContaminant
addDissimilarity	getDissimilarity
addDissimilarity,SummarizedExperiment-method	getDissimilarity
addDivergence	addDivergence
addDivergence,SummarizedExperiment-method	addDivergence
addDominant	getDominant
addDominant,SummarizedExperiment-method	getDominant
addDPCoA	runDPCoA
addHierarchyTree	hierarchy-tree
addHierarchyTree,SummarizedExperiment-method	hierarchy-tree
addJointRPCA	getRPCA
addJointRPCA,MultiAssayExperiment-method	getRPCA
addJointRPCA,SingleCellExperiment-method	getRPCA
addLDA	addLDA
addLDA,SummarizedExperiment-method	addLDA
addMDS	addMDS
addMDS,SingleCellExperiment-method	addMDS
addMediation	getMediation
addMediation,SummarizedExperiment-method	getMediation
addNMDS	runNMDS
addNMF	addNMF
addNMF,SummarizedExperiment-method	addNMF
addNotContaminantQC	isContaminant
addNotContaminantQC,SummarizedExperiment-method	isContaminant
addPERMANOVA	getPERMANOVA
addPERMANOVA,SummarizedExperiment-method	getPERMANOVA
addPerSampleDominantFeatures	deprecate
addPerSampleDominantFeatures,SummarizedExperiment-method	deprecate
addPerSampleDominantTaxa	deprecate
addPerSampleDominantTaxa,SummarizedExperiment-method	deprecate
addPrevalence	getPrevalence
addPrevalence,SummarizedExperiment-method	getPrevalence
addPrevalentAbundance	getPrevalence
addPrevalentAbundance,SummarizedExperiment-method	getPrevalence
addRDA	runCCA
addRDA,SingleCellExperiment-method	runCCA
addRPCA	getRPCA
addRPCA,SummarizedExperiment-method	getRPCA
addTaxonomyTree	deprecate
addTaxonomyTree,SummarizedExperiment-method	deprecate
agglomerate-methods	agglomerate-methods
agglomerateByModule	agglomerate-methods
agglomerateByModule,SummarizedExperiment-method	agglomerate-methods
agglomerateByPrevalence	agglomerateByPrevalence
agglomerateByPrevalence,SummarizedExperiment-method	agglomerateByPrevalence
agglomerateByPrevalence,TreeSummarizedExperiment-method	agglomerateByPrevalence
agglomerateByRank	agglomerate-methods
agglomerateByRank,SingleCellExperiment-method	agglomerate-methods
agglomerateByRank,SummarizedExperiment-method	agglomerate-methods
agglomerateByRank,TreeSummarizedExperiment-method	agglomerate-methods
agglomerateByRanks	agglomerate-methods
agglomerateByRanks,SingleCellExperiment-method	agglomerate-methods
agglomerateByRanks,SummarizedExperiment-method	agglomerate-methods
agglomerateByRanks,TreeSummarizedExperiment-method	agglomerate-methods
agglomerateByVariable	agglomerate-methods
agglomerateByVariable,SummarizedExperiment-method	agglomerate-methods
agglomerateByVariable,TreeSummarizedExperiment-method	agglomerate-methods
bestDMNFit	calculateDMN
bestDMNFit,SummarizedExperiment-method	calculateDMN
calculateCCA	runCCA
calculateDMN	calculateDMN
calculateDMN,ANY-method	calculateDMN
calculateDMN,SummarizedExperiment-method	calculateDMN
calculateDMNgroup	calculateDMN
calculateDMNgroup,ANY-method	calculateDMN
calculateDMNgroup,SummarizedExperiment-method	calculateDMN
calculateDPCoA	runDPCoA
calculateJSD	deprecate
calculateJSD,ANY-method	deprecate
calculateNMDS	runNMDS
calculateOverlap	deprecate
calculateOverlap,ANY-method	deprecate
calculateRDA	runCCA
calculateUnifrac	deprecate
calculateUnifrac,ANY-method	deprecate
checkTaxonomy	taxonomy-methods
checkTaxonomy,SummarizedExperiment-method	taxonomy-methods
cluster	deprecate
cluster,SummarizedExperiment-method	deprecate
convertFromBIOM	importBIOM
convertFromDADA2	convertFromDADA2
convertFromPhyloseq	convertFromPhyloseq
convertToBIOM	importBIOM
convertToBIOM,SummarizedExperiment-method	importBIOM
convertToPhyloseq	convertFromPhyloseq
convertToPhyloseq,SummarizedExperiment-method	convertFromPhyloseq
convertToPhyloseq,TreeSummarizedExperiment-method	convertFromPhyloseq
countDominantFeatures	deprecate
countDominantFeatures,SummarizedExperiment-method	deprecate
countDominantTaxa	deprecate
countDominantTaxa,SummarizedExperiment-method	deprecate
deprecate	deprecate
dmn_se	dmn_se
enterotype	enterotype
esophagus	esophagus
estimateDivergence	deprecate
estimateDivergence,SummarizedExperiment-method	deprecate
estimateDiversity	deprecate
estimateDiversity,ANY-method	deprecate
estimateDominance	deprecate
estimateDominance,ANY-method	deprecate
estimateEvenness	deprecate
estimateEvenness,ANY-method	deprecate
estimateFaith	deprecate
estimateFaith,ANY-method	deprecate
estimateRichness	deprecate
estimateRichness,ANY-method	deprecate
full_join	deprecate
full_join,ANY-method	deprecate
getAbundanceClass	getAbundant
getAbundanceClass,ANY-method	getAbundant
getAbundanceClass,SingleCellExperiment-method	getAbundant
getAbundanceClass,SummarizedExperiment-method	getAbundant
getAbundant	getAbundant
getAbundant,ANY-method	getAbundant
getAbundant,SingleCellExperiment-method	getAbundant
getAbundant,SummarizedExperiment-method	getAbundant
getAlpha	addAlpha
getAlpha,SummarizedExperiment-method	addAlpha
getBestDMNFit	calculateDMN
getBestDMNFit,SummarizedExperiment-method	calculateDMN
getCCA	runCCA
getCCA,ANY-method	runCCA
getCCA,SummarizedExperiment-method	runCCA
getCluster	addCluster
getCluster,ANY-method	addCluster
getCluster,SingleCellExperiment-method	addCluster
getCluster,SummarizedExperiment-method	addCluster
getConditionallyLowAbundant	getAbundant
getConditionallyLowAbundant,ANY-method	getAbundant
getConditionallyLowAbundant,SingleCellExperiment-method	getAbundant
getConditionallyLowAbundant,SummarizedExperiment-method	getAbundant
getCrossAssociation	getCrossAssociation
getCrossAssociation,MultiAssayExperiment-method	getCrossAssociation
getCrossAssociation,SummarizedExperiment-method	getCrossAssociation
getDissimilarity	getDissimilarity
getDissimilarity,ANY-method	getDissimilarity
getDissimilarity,SummarizedExperiment-method	getDissimilarity
getDissimilarity,TreeSummarizedExperiment-method	getDissimilarity
getDivergence	addDivergence
getDivergence,SummarizedExperiment-method	addDivergence
getDMN	calculateDMN
getDMN,SummarizedExperiment-method	calculateDMN
getDominant	getDominant
getDominant,SummarizedExperiment-method	getDominant
getDPCoA	runDPCoA
getDPCoA,ANY,ANY-method	runDPCoA
getDPCoA,TreeSummarizedExperiment,missing-method	runDPCoA
getExperimentCrossAssociation	deprecate
getExperimentCrossAssociation,MultiAssayExperiment-method	deprecate
getExperimentCrossAssociation,SummarizedExperiment-method	deprecate
getExperimentCrossCorrelation	deprecate
getExperimentCrossCorrelation,ANY-method	deprecate
getHierarchyTree	hierarchy-tree
getHierarchyTree,SummarizedExperiment-method	hierarchy-tree
getJointRPCA	getRPCA
getJointRPCA,MultiAssayExperiment-method	getRPCA
getJointRPCA,SingleCellExperiment-method	getRPCA
getLDA	addLDA
getLDA,SummarizedExperiment-method	addLDA
getLowAbundant	getAbundant
getLowAbundant,ANY-method	getAbundant
getLowAbundant,SingleCellExperiment-method	getAbundant
getLowAbundant,SummarizedExperiment-method	getAbundant
getMDS	addMDS
getMDS,SingleCellExperiment-method	addMDS
getMDS,TreeSummarizedExperiment-method	addMDS
getMediation	getMediation
getMediation,SummarizedExperiment-method	getMediation
getNMDS	runNMDS
getNMDS,ANY-method	runNMDS
getNMDS,SingleCellExperiment-method	runNMDS
getNMDS,SummarizedExperiment-method	runNMDS
getNMF	addNMF
getNMF,SummarizedExperiment-method	addNMF
getPermanentlyLowAbundant	getAbundant
getPermanentlyLowAbundant,ANY-method	getAbundant
getPermanentlyLowAbundant,SingleCellExperiment-method	getAbundant
getPermanentlyLowAbundant,SummarizedExperiment-method	getAbundant
getPERMANOVA	getPERMANOVA
getPERMANOVA,ANY-method	getPERMANOVA
getPERMANOVA,SingleCellExperiment-method	getPERMANOVA
getPERMANOVA,SummarizedExperiment-method	getPERMANOVA
getPrevalence	getPrevalence
getPrevalence,ANY-method	getPrevalence
getPrevalence,SummarizedExperiment-method	getPrevalence
getPrevalent	getPrevalence
getPrevalent,ANY-method	getPrevalence
getPrevalent,SummarizedExperiment-method	getPrevalence
getPrevalentAbundance	getPrevalence
getPrevalentAbundance,ANY-method	getPrevalence
getPrevalentAbundance,SummarizedExperiment-method	getPrevalence
getPrevalentFeatures	deprecate
getPrevalentFeatures,ANY-method	deprecate
getPrevalentFeatures,SummarizedExperiment-method	deprecate
getPrevalentTaxa	deprecate
getPrevalentTaxa,ANY-method	deprecate
getPrevalentTaxa,SummarizedExperiment-method	deprecate
getRare	getPrevalence
getRare,ANY-method	getPrevalence
getRare,SummarizedExperiment-method	getPrevalence
getRareFeatures	deprecate
getRareFeatures,ANY-method	deprecate
getRareFeatures,SummarizedExperiment-method	deprecate
getRareTaxa	deprecate
getRareTaxa,ANY-method	deprecate
getRareTaxa,SummarizedExperiment-method	deprecate
getRDA	runCCA
getRDA,ANY-method	runCCA
getRDA,SummarizedExperiment-method	runCCA
getReducedDimAttribute	utilization_functions
getReducedDimAttribute,SingleCellExperiment-method	utilization_functions
getRPCA	getRPCA
getRPCA,SingleCellExperiment-method	getRPCA
getRPCA,SummarizedExperiment-method	getRPCA
getTaxonomyLabels	taxonomy-methods
getTaxonomyLabels,SummarizedExperiment-method	taxonomy-methods
getTaxonomyRanks	taxonomy-methods
getTop	summary
getTop,SummarizedExperiment-method	summary
getTopFeatures	deprecate
getTopFeatures,SummarizedExperiment-method	deprecate
getTopTaxa	deprecate
getTopTaxa,SummarizedExperiment-method	deprecate
getUnique	summary
getUnique,SummarizedExperiment-method	summary
getUniqueFeatures	deprecate
getUniqueFeatures,SummarizedExperiment-method	deprecate
getUniqueTaxa	deprecate
getUniqueTaxa,SummarizedExperiment-method	deprecate
GlobalPatterns	GlobalPatterns
hierarchy-tree	hierarchy-tree
HintikkaXOData	HintikkaXOData
ibdmdb	ibdmdb
IdTaxaToDataFrame	taxonomy-methods
importBIOM	importBIOM
importHUMAnN	importHUMAnN
importMetaPhlAn	importMetaPhlAn
importMothur	importMothur
importQIIME2	importQIIME2
importQZA	importQIIME2
importTaxpasta	importTaxpasta
inner_join	deprecate
inner_join,ANY-method	deprecate
isContaminant	isContaminant
isContaminant,SummarizedExperiment-method	isContaminant
isNotContaminant,SummarizedExperiment-method	isContaminant
left_join	deprecate
left_join,ANY-method	deprecate
loadFromBiom	deprecate
loadFromHumann	deprecate
loadFromMetaphlan	deprecate
loadFromMothur	deprecate
loadFromQIIME2	deprecate
makePhyloseqFromTreeSE	deprecate
makePhyloseqFromTreeSE,SummarizedExperiment-method	deprecate
makePhyloseqFromTreeSE,TreeSummarizedExperiment-method	deprecate
makePhyloseqFromTreeSummarizedExperiment	deprecate
makePhyloseqFromTreeSummarizedExperiment,ANY-method	deprecate
makeTreeSEFromBiom	deprecate
makeTreeSEFromDADA2	deprecate
makeTreeSEFromPhyloseq	deprecate
makeTreeSummarizedExperimentFromBiom	deprecate
makeTreeSummarizedExperimentFromDADA2	deprecate
makeTreeSummarizedExperimentFromPhyloseq	deprecate
makeTreeSummarizedExperimentFromPhyloseq,ANY-method	deprecate
mapTaxonomy	taxonomy-methods
mapTaxonomy,SummarizedExperiment-method	taxonomy-methods
meltAssay	deprecate
meltAssay,SummarizedExperiment-method	deprecate
meltSE	meltSE
meltSE,SingleCellExperiment-method	meltSE
meltSE,SummarizedExperiment-method	meltSE
mergeCols	deprecate
mergeCols,SummarizedExperiment-method	deprecate
mergeCols,TreeSummarizedExperiment-method	deprecate
mergeFeatures	deprecate
mergeFeatures,SummarizedExperiment-method	deprecate
mergeFeatures,TreeSummarizedExperiment-method	deprecate
mergeFeaturesByPrevalence	deprecate
mergeFeaturesByPrevalence,SummarizedExperiment-method	deprecate
mergeFeaturesByRank	deprecate
mergeFeaturesByRank,SingleCellExperiment-method	deprecate
mergeFeaturesByRank,SummarizedExperiment-method	deprecate
mergeFeaturesByRank,TreeSummarizedExperiment-method	deprecate
mergeRows	deprecate
mergeRows,SummarizedExperiment-method	deprecate
mergeRows,TreeSummarizedExperiment-method	deprecate
mergeSamples	deprecate
mergeSamples,SummarizedExperiment-method	deprecate
mergeSamples,TreeSummarizedExperiment-method	deprecate
mergeSEs	mergeSEs
mergeSEs,list-method	mergeSEs
mergeSEs,SimpleList-method	mergeSEs
mergeSEs,SummarizedExperiment-method	mergeSEs
mia	mia-package
mia-datasets	mia-datasets
peerj13075	peerj13075
performDMNgroupCV	calculateDMN
performDMNgroupCV,ANY-method	calculateDMN
performDMNgroupCV,SummarizedExperiment-method	calculateDMN
perSampleDominantFeatures	deprecate
perSampleDominantFeatures,SummarizedExperiment-method	deprecate
perSampleDominantTaxa	deprecate
perSampleDominantTaxa,SummarizedExperiment-method	deprecate
plotNMDS	deprecate
rarefyAssay	rarefyAssay
rarefyAssay,SummarizedExperiment-method	rarefyAssay
readQZA	deprecate
relabundance	deprecate
relabundance,SummarizedExperiment-method	deprecate
relabundance<-	deprecate
relabundance<-,SummarizedExperiment-method	deprecate
relAbundanceCounts	deprecate
relAbundanceCounts,SummarizedExperiment-method	deprecate
right_join	deprecate
right_join,ANY-method	deprecate
runCCA	runCCA
runDMN	calculateDMN
runDPCoA	runDPCoA
runJSD	deprecate
runJSD,SummarizedExperiment-method	deprecate
runNMDS	runNMDS
runOverlap	deprecate
runOverlap,SummarizedExperiment-method	deprecate
runRDA	runCCA
runUnifrac	deprecate
setTaxonomyRanks	taxonomy-methods
splitByRanks	agglomerate-methods
splitOn	splitOn
splitOn,SingleCellExperiment-method	splitOn
splitOn,SummarizedExperiment-method	splitOn
splitOn,TreeSummarizedExperiment-method	splitOn
subsampleCounts	deprecate
subsampleCounts,SummarizedExperiment-method	deprecate
subsetByPrevalent	getPrevalence
subsetByPrevalent,SummarizedExperiment-method	getPrevalence
subsetByPrevalent,TreeSummarizedExperiment-method	getPrevalence
subsetByPrevalentFeatures	deprecate
subsetByPrevalentFeatures,ANY-method	deprecate
subsetByPrevalentTaxa	deprecate
subsetByPrevalentTaxa,ANY-method	deprecate
subsetByRare	getPrevalence
subsetByRare,SummarizedExperiment-method	getPrevalence
subsetByRare,TreeSummarizedExperiment-method	getPrevalence
subsetByRareFeatures	deprecate
subsetByRareFeatures,ANY-method	deprecate
subsetByRareTaxa	deprecate
subsetByRareTaxa,ANY-method	deprecate
subsetFeatures	deprecate
subsetFeatures,SummarizedExperiment-method	deprecate
subsetSamples	deprecate
subsetSamples,SummarizedExperiment-method	deprecate
subsetTaxa	deprecate
subsetTaxa,SummarizedExperiment-method	deprecate
summarizeDominance	summary
summarizeDominance,SummarizedExperiment-method	summary
summary	summary
summary,SummarizedExperiment-method	summary
taxonomy-methods	taxonomy-methods
taxonomyRankEmpty	taxonomy-methods
taxonomyRankEmpty,SummarizedExperiment-method	taxonomy-methods
taxonomyRanks	taxonomy-methods
taxonomyRanks,SummarizedExperiment-method	taxonomy-methods
taxonomyTree	deprecate
taxonomyTree,SummarizedExperiment-method	deprecate
Tengeler2020	Tengeler2020
testExperimentCrossAssociation	deprecate
testExperimentCrossAssociation,ANY-method	deprecate
testExperimentCrossCorrelation	deprecate
testExperimentCrossCorrelation,ANY-method	deprecate
Tito2024QMP	Tito2024QMP
transformAssay	transformAssay
transformAssay,SingleCellExperiment-method	transformAssay
transformAssay,SummarizedExperiment-method	transformAssay
transformCounts	deprecate
transformFeatures	deprecate
transformFeatures,SummarizedExperiment-method	deprecate
transformSamples	deprecate
transformSamples,SummarizedExperiment-method	deprecate
twins	dmn_se
unsplitByRanks	agglomerate-methods
unsplitByRanks,SingleCellExperiment-method	agglomerate-methods
unsplitByRanks,TreeSummarizedExperiment-method	agglomerate-methods
unsplitOn	splitOn
unsplitOn,list-method	splitOn
unsplitOn,SimpleList-method	splitOn
unsplitOn,SingleCellExperiment-method	splitOn
utilization_functions	utilization_functions
ZTransform	deprecate
ZTransform,SummarizedExperiment-method	deprecate
