mia-package	mia-package
addCluster	addCluster
addCluster,SummarizedExperiment-method	addCluster
addContaminantQC	isContaminant
addContaminantQC,SummarizedExperiment-method	isContaminant
addDivergence	addDivergence
addDivergence,SummarizedExperiment-method	addDivergence
addHierarchyTree	hierarchy-tree
addHierarchyTree,SummarizedExperiment-method	hierarchy-tree
addNotContaminantQC	isContaminant
addNotContaminantQC,SummarizedExperiment-method	isContaminant
addPerSampleDominantFeatures	perSampleDominantTaxa
addPerSampleDominantFeatures,SummarizedExperiment-method	perSampleDominantTaxa
addPerSampleDominantTaxa	perSampleDominantTaxa
addPerSampleDominantTaxa,SummarizedExperiment-method	perSampleDominantTaxa
addTaxonomyTree	deprecate
addTaxonomyTree,SummarizedExperiment-method	deprecate
agglomerate-methods	agglomerate-methods
agglomerateByPrevalence	agglomerate-methods
agglomerateByPrevalence,SummarizedExperiment-method	agglomerate-methods
agglomerateByRank	agglomerate-methods
agglomerateByRank,SingleCellExperiment-method	agglomerate-methods
agglomerateByRank,SummarizedExperiment-method	agglomerate-methods
agglomerateByRank,TreeSummarizedExperiment-method	agglomerate-methods
bestDMNFit	calculateDMN
bestDMNFit,SummarizedExperiment-method	calculateDMN
calculateCCA	runCCA
calculateCCA,ANY-method	runCCA
calculateCCA,SummarizedExperiment-method	runCCA
calculateDMN	calculateDMN
calculateDMN,ANY-method	calculateDMN
calculateDMN,SummarizedExperiment-method	calculateDMN
calculateDMNgroup	calculateDMN
calculateDMNgroup,ANY-method	calculateDMN
calculateDMNgroup,SummarizedExperiment-method	calculateDMN
calculateDPCoA	runDPCoA
calculateDPCoA,ANY,ANY-method	runDPCoA
calculateDPCoA,TreeSummarizedExperiment,missing-method	runDPCoA
calculateJSD	calculateJSD
calculateJSD,ANY-method	calculateJSD
calculateJSD,SummarizedExperiment-method	calculateJSD
calculateNMDS	runNMDS
calculateNMDS,ANY-method	runNMDS
calculateNMDS,SingleCellExperiment-method	runNMDS
calculateNMDS,SummarizedExperiment-method	runNMDS
calculateOverlap	calculateOverlap
calculateOverlap,SummarizedExperiment-method	calculateOverlap
calculateRDA	runCCA
calculateRDA,ANY-method	runCCA
calculateRDA,SummarizedExperiment-method	runCCA
calculateUnifrac	calculateUnifrac
calculateUnifrac,ANY,phylo-method	calculateUnifrac
calculateUnifrac,TreeSummarizedExperiment,missing-method	calculateUnifrac
checkTaxonomy	taxonomy-methods
checkTaxonomy,SummarizedExperiment-method	taxonomy-methods
cluster	deprecate
cluster,SummarizedExperiment-method	deprecate
countDominantFeatures	summaries
countDominantFeatures,SummarizedExperiment-method	summaries
countDominantTaxa	summaries
countDominantTaxa,SummarizedExperiment-method	summaries
deprecate	deprecate
dmn_se	dmn_se
enterotype	enterotype
esophagus	esophagus
estimateDivergence	deprecate
estimateDivergence,SummarizedExperiment-method	deprecate
estimateDiversity	estimateDiversity
estimateDiversity,SummarizedExperiment-method	estimateDiversity
estimateDiversity,TreeSummarizedExperiment-method	estimateDiversity
estimateDominance	estimateDominance
estimateDominance,SummarizedExperiment-method	estimateDominance
estimateEvenness	estimateEvenness
estimateEvenness,SummarizedExperiment-method	estimateEvenness
estimateFaith	estimateDiversity
estimateFaith,SummarizedExperiment,phylo-method	estimateDiversity
estimateFaith,TreeSummarizedExperiment,missing-method	estimateDiversity
estimateRichness	estimateRichness
estimateRichness,SummarizedExperiment-method	estimateRichness
full_join	deprecate
full_join,ANY-method	deprecate
getBestDMNFit	calculateDMN
getBestDMNFit,SummarizedExperiment-method	calculateDMN
getDMN	calculateDMN
getDMN,SummarizedExperiment-method	calculateDMN
getExperimentCrossAssociation	getExperimentCrossAssociation
getExperimentCrossAssociation,MultiAssayExperiment-method	getExperimentCrossAssociation
getExperimentCrossAssociation,SummarizedExperiment-method	getExperimentCrossAssociation
getExperimentCrossCorrelation	getExperimentCrossAssociation
getExperimentCrossCorrelation,ANY-method	getExperimentCrossAssociation
getHierarchyTree	hierarchy-tree
getHierarchyTree,SummarizedExperiment-method	hierarchy-tree
getPrevalence	getPrevalence
getPrevalence,ANY-method	getPrevalence
getPrevalence,SummarizedExperiment-method	getPrevalence
getPrevalentAbundance	getPrevalence
getPrevalentAbundance,ANY-method	getPrevalence
getPrevalentAbundance,SummarizedExperiment-method	getPrevalence
getPrevalentFeatures	getPrevalence
getPrevalentFeatures,ANY-method	getPrevalence
getPrevalentFeatures,SummarizedExperiment-method	getPrevalence
getPrevalentTaxa	getPrevalence
getPrevalentTaxa,ANY-method	getPrevalence
getRareFeatures	getPrevalence
getRareFeatures,ANY-method	getPrevalence
getRareFeatures,SummarizedExperiment-method	getPrevalence
getRarePrevalentTaxa	getPrevalence
getRareTaxa	getPrevalence
getRareTaxa,ANY-method	getPrevalence
getTaxonomyLabels	taxonomy-methods
getTaxonomyLabels,SummarizedExperiment-method	taxonomy-methods
getTaxonomyRanks	taxonomy-methods
getTopFeatures	summaries
getTopFeatures,SummarizedExperiment-method	summaries
getTopTaxa	summaries
getTopTaxa,SummarizedExperiment-method	summaries
getUniqueFeatures	summaries
getUniqueFeatures,SummarizedExperiment-method	summaries
getUniqueTaxa	summaries
getUniqueTaxa,SummarizedExperiment-method	summaries
GlobalPatterns	GlobalPatterns
hierarchy-tree	hierarchy-tree
HintikkaXOData	HintikkaXOData
IdTaxaToDataFrame	taxonomy-methods
importBIOM	makeTreeSEFromBiom
importHUMAnN	importHUMAnN
importMetaPhlAn	importMetaPhlAn
importMothur	importMothur
importQIIME2	importQIIME2
importQZA	importQIIME2
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	makePhyloseqFromTreeSE
makePhyloseqFromTreeSE,SummarizedExperiment-method	makePhyloseqFromTreeSE
makePhyloseqFromTreeSE,TreeSummarizedExperiment-method	makePhyloseqFromTreeSE
makePhyloseqFromTreeSummarizedExperiment	makePhyloseqFromTreeSE
makePhyloseqFromTreeSummarizedExperiment,ANY-method	makePhyloseqFromTreeSE
makeTreeSEFromBiom	makeTreeSEFromBiom
makeTreeSEFromDADA2	makeTreeSEFromDADA2
makeTreeSEFromPhyloseq	makeTreeSEFromPhyloseq
makeTreeSummarizedExperimentFromBiom	makeTreeSEFromBiom
makeTreeSummarizedExperimentFromDADA2	makeTreeSEFromDADA2
makeTreeSummarizedExperimentFromPhyloseq	makeTreeSEFromPhyloseq
makeTreeSummarizedExperimentFromPhyloseq,ANY-method	makeTreeSEFromPhyloseq
mapTaxonomy	taxonomy-methods
mapTaxonomy,SummarizedExperiment-method	taxonomy-methods
meltAssay	meltAssay
meltAssay,SummarizedExperiment-method	meltAssay
merge-methods	merge-methods
mergeCols	merge-methods
mergeCols,SummarizedExperiment-method	merge-methods
mergeCols,TreeSummarizedExperiment-method	merge-methods
mergeFeatures	merge-methods
mergeFeatures,SummarizedExperiment-method	merge-methods
mergeFeatures,TreeSummarizedExperiment-method	merge-methods
mergeFeaturesByPrevalence	deprecate
mergeFeaturesByPrevalence,SummarizedExperiment-method	deprecate
mergeFeaturesByRank	agglomerate-methods
mergeFeaturesByRank,SingleCellExperiment-method	agglomerate-methods
mergeFeaturesByRank,SummarizedExperiment-method	agglomerate-methods
mergeFeaturesByRank,TreeSummarizedExperiment-method	agglomerate-methods
mergeRows	merge-methods
mergeRows,SummarizedExperiment-method	merge-methods
mergeRows,TreeSummarizedExperiment-method	merge-methods
mergeSamples	merge-methods
mergeSamples,SummarizedExperiment-method	merge-methods
mergeSamples,TreeSummarizedExperiment-method	merge-methods
mergeSEs	mergeSEs
mergeSEs,list-method	mergeSEs
mergeSEs,SimpleList-method	mergeSEs
mergeSEs,SummarizedExperiment-method	mergeSEs
mergeSmaples	merge-methods
mia	mia-package
mia-datasets	mia-datasets
peerj13075	peerj13075
performDMNgroupCV	calculateDMN
performDMNgroupCV,ANY-method	calculateDMN
performDMNgroupCV,SummarizedExperiment-method	calculateDMN
perSampleDominantFeatures	perSampleDominantTaxa
perSampleDominantFeatures,SummarizedExperiment-method	perSampleDominantTaxa
perSampleDominantTaxa	perSampleDominantTaxa
perSampleDominantTaxa,SummarizedExperiment-method	perSampleDominantTaxa
plotNMDS	deprecate
rarifyCounts	subsampleCounts
readQZA	deprecate
relabundance	relabundance
relabundance,SummarizedExperiment-method	relabundance
relabundance<-	relabundance
relabundance<-,SummarizedExperiment-method	relabundance
relAbundanceCounts	transformAssay
relAbundanceCounts,SummarizedExperiment-method	transformAssay
right_join	deprecate
right_join,ANY-method	deprecate
runCCA	runCCA
runCCA,SingleCellExperiment-method	runCCA
runDMN	calculateDMN
runDPCoA	runDPCoA
runJSD	calculateJSD
runNMDS	runNMDS
runOverlap	calculateOverlap
runOverlap,SummarizedExperiment-method	calculateOverlap
runRDA	runCCA
runRDA,SingleCellExperiment-method	runCCA
runUnifrac	calculateUnifrac
setTaxonomyRanks	taxonomy-methods
splitByRanks	splitByRanks
splitByRanks,SingleCellExperiment-method	splitByRanks
splitByRanks,SummarizedExperiment-method	splitByRanks
splitByRanks,TreeSummarizedExperiment-method	splitByRanks
splitOn	splitOn
splitOn,SingleCellExperiment-method	splitOn
splitOn,SummarizedExperiment-method	splitOn
splitOn,TreeSummarizedExperiment-method	splitOn
subsampleCounts	subsampleCounts
subsampleCounts,SummarizedExperiment-method	subsampleCounts
subsetByPrevalentFeatures	getPrevalence
subsetByPrevalentFeatures,SummarizedExperiment-method	getPrevalence
subsetByPrevalentTaxa	getPrevalence
subsetByPrevalentTaxa,ANY-method	getPrevalence
subsetByRareFeatures	getPrevalence
subsetByRareFeatures,SummarizedExperiment-method	getPrevalence
subsetByRareTaxa	getPrevalence
subsetByRareTaxa,ANY-method	getPrevalence
subsetFeatures	subsetSamples
subsetFeatures,SummarizedExperiment-method	subsetSamples
subsetSamples	subsetSamples
subsetSamples,SummarizedExperiment-method	subsetSamples
subsetTaxa	subsetSamples
subsetTaxa,SummarizedExperiment-method	subsetSamples
summaries	summaries
summary,SummarizedExperiment-method	summaries
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
TAXONOMY_RANKS	taxonomy-methods
Tengeler2020	Tengeler2020
testExperimentCrossAssociation	getExperimentCrossAssociation
testExperimentCrossAssociation,ANY-method	getExperimentCrossAssociation
testExperimentCrossCorrelation	getExperimentCrossAssociation
testExperimentCrossCorrelation,ANY-method	getExperimentCrossAssociation
transformAssay	transformAssay
transformAssay,SummarizedExperiment-method	transformAssay
transformCounts	transformAssay
transformFeatures	transformAssay
transformFeatures,SummarizedExperiment-method	transformAssay
transformSamples	transformAssay
transformSamples,SummarizedExperiment-method	transformAssay
twins	dmn_se
unsplitByRanks	splitByRanks
unsplitByRanks,SingleCellExperiment-method	splitByRanks
unsplitByRanks,TreeSummarizedExperiment-method	splitByRanks
unsplitOn	splitOn
unsplitOn,list-method	splitOn
unsplitOn,SimpleList-method	splitOn
unsplitOn,SingleCellExperiment-method	splitOn
ZTransform	transformAssay
ZTransform,SummarizedExperiment-method	transformAssay
