mia-package	mia-package
addContaminantQC	isContaminant
addContaminantQC,SummarizedExperiment-method	isContaminant
addNotContaminantQC	isContaminant
addNotContaminantQC,SummarizedExperiment-method	isContaminant
addPerSampleDominantTaxa	perSampleDominantTaxa
addPerSampleDominantTaxa,SummarizedExperiment-method	perSampleDominantTaxa
addTaxonomyTree	taxonomy-methods
addTaxonomyTree,SummarizedExperiment-method	taxonomy-methods
agglomerate-methods	agglomerate-methods
agglomerateByPrevalence	getPrevalence
agglomerateByPrevalence,SummarizedExperiment-method	getPrevalence
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
calculateDistance	calculateDistance
calculateDistance,ANY-method	calculateDistance
calculateDistance,SummarizedExperiment-method	calculateDistance
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	calculateUnifrac
calculateUnifrac,ANY,phylo-method	calculateUnifrac
calculateUniFrac,ANY-method	calculateUnifrac
calculateUnifrac,TreeSummarizedExperiment,missing-method	calculateUnifrac
checkTaxonomy	taxonomy-methods
checkTaxonomy,SummarizedExperiment-method	taxonomy-methods
countDominantTaxa	summaries
countDominantTaxa,SummarizedExperiment-method	summaries
dmn_se	mia-datasets
dmn_se,	mia-datasets
enterotype	mia-datasets
esophagus	mia-datasets
estimateDivergence	estimateDivergence
estimateDivergence,SummarizedExperiment-method	estimateDivergence
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
getAbundance	getAbundance
getAbundanceFeature	getAbundance
getAbundanceFeature,SummarizedExperiment-method	getAbundance
getAbundanceSample	getAbundance
getAbundanceSample,SummarizedExperiment-method	getAbundance
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
getPrevalence	getPrevalence
getPrevalence,ANY-method	getPrevalence
getPrevalence,SummarizedExperiment-method	getPrevalence
getPrevalentAbundance	getPrevalence
getPrevalentAbundance,ANY-method	getPrevalence
getPrevalentAbundance,SummarizedExperiment-method	getPrevalence
getPrevalentTaxa	getPrevalence
getPrevalentTaxa,ANY-method	getPrevalence
getPrevalentTaxa,SummarizedExperiment-method	getPrevalence
getRareTaxa	getPrevalence
getRareTaxa,ANY-method	getPrevalence
getRareTaxa,SummarizedExperiment-method	getPrevalence
getTaxonomyLabels	taxonomy-methods
getTaxonomyLabels,SummarizedExperiment-method	taxonomy-methods
getTopTaxa	summaries
getTopTaxa,SummarizedExperiment-method	summaries
getUniqueTaxa	summaries
getUniqueTaxa,SummarizedExperiment-method	summaries
GlobalPatterns	mia-datasets
IdTaxaToDataFrame	taxonomy-methods
isContaminant	isContaminant
isContaminant,SummarizedExperiment-method	isContaminant
isNotContaminant,SummarizedExperiment-method	isContaminant
loadFromBiom	makeSummarizedExperimentFromBiom
loadFromMetaphlan	loadFromMetaphlan
loadFromMothur	loadFromMothur
loadFromQIIME2	loadFromQIIME2
makePhyloseqFromTreeSummarizedExperiment	makePhyloseqFromTreeSummarizedExperiment
makePhyloseqFromTreeSummarizedExperiment,SummarizedExperiment-method	makePhyloseqFromTreeSummarizedExperiment
makePhyloseqFromTreeSummarizedExperiment,TreeSummarizedExperiment-method	makePhyloseqFromTreeSummarizedExperiment
makeSummarizedExperimentFromBiom	makeSummarizedExperimentFromBiom
makeTreeSummarizedExperimentFromDADA2	makeTreeSummarizedExperimentFromDADA2
makeTreeSummarizedExperimentFromPhyloseq	makeTreeSummarizedExperimentFromPhyloseq
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
mergeRows	merge-methods
mergeRows,SummarizedExperiment-method	merge-methods
mergeRows,TreeSummarizedExperiment-method	merge-methods
mia-datasets	mia-datasets
performDMNgroupCV	calculateDMN
performDMNgroupCV,ANY-method	calculateDMN
performDMNgroupCV,SummarizedExperiment-method	calculateDMN
perSampleDominantTaxa	perSampleDominantTaxa
perSampleDominantTaxa,SummarizedExperiment-method	perSampleDominantTaxa
plotNMDS	runNMDS
rarifyCounts	subsampleCounts
readQZA	loadFromQIIME2
relabundance	relabundance
relabundance,SummarizedExperiment-method	relabundance
relabundance<-	relabundance
relabundance<-,SummarizedExperiment-method	relabundance
relAbundanceCounts	transformCounts
relAbundanceCounts,SummarizedExperiment-method	transformCounts
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
splitByRanks	splitByRanks
splitByRanks,SingleCellExperiment-method	splitByRanks
splitByRanks,SummarizedExperiment-method	splitByRanks
splitByRanks,TreeSummarizedExperiment-method	splitByRanks
subsampleCounts	subsampleCounts
subsampleCounts,SummarizedExperiment-method	subsampleCounts
subsetByPrevalentTaxa	getPrevalence
subsetByPrevalentTaxa,SummarizedExperiment-method	getPrevalence
subsetByRareTaxa	getPrevalence
subsetByRareTaxa,SummarizedExperiment-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	taxonomy-methods
taxonomyTree,SummarizedExperiment-method	taxonomy-methods
TAXONOMY_RANKS	taxonomy-methods
testExperimentCrossAssociation	getExperimentCrossAssociation
testExperimentCrossAssociation,ANY-method	getExperimentCrossAssociation
testExperimentCrossCorrelation	getExperimentCrossAssociation
testExperimentCrossCorrelation,ANY-method	getExperimentCrossAssociation
transformCounts	transformCounts
transformCounts,SummarizedExperiment-method	transformCounts
transformFeatures	transformCounts
transformFeatures,SummarizedExperiment-method	transformCounts
transformSamples	transformCounts
transformSamples,SummarizedExperiment-method	transformCounts
twins	mia-datasets
unsplitByRanks	splitByRanks
unsplitByRanks,SingleCellExperiment-method	splitByRanks
unsplitByRanks,TreeSummarizedExperiment-method	splitByRanks
ZTransform	transformCounts
ZTransform,SummarizedExperiment-method	transformCounts
