agglomerate-methods     Agglomerate data using taxonomic information
calculateDMN            Dirichlet-Multinomial Mixture Model: Machine
                        Learning for Microbiome Data
calculateJSD            Calculate the Jensen-Shannon Divergence
calculateOverlap        Estimate overlap
calculateUnifrac        Calculate weighted or unweighted (Fast) Unifrac
                        distance
estimateDivergence      Estimate divergence
estimateDiversity       Estimate (alpha) diversity measures
estimateDominance       Estimate dominance measures
estimateEvenness        Estimate Evenness measures
estimateRichness        Estimate richness measures
getAbundance            Get abundance values by "SampleID" or
                        "FeatureID"
getExperimentCrossAssociation
                        Calculate correlations between features of two
                        experiments.
getPrevalence           Calculation prevalence information for features
                        across samples
isContaminant           decontam functions
loadFromMetaphlan       Import Metaphlan results to
                        'TreeSummarizedExperiment'
loadFromMothur          Import Mothur results as a
                        'TreeSummarizedExperiment'
loadFromQIIME2          Import QIIME2 results to
                        'TreeSummarizedExperiment'
makePhyloseqFromTreeSE
                        Create a phyloseq object from a
                        TreeSummarizedExperiment object
makeTreeSEFromBiom      Loading a biom file
makeTreeSEFromDADA2     Coerce 'DADA2' results to
                        'TreeSummarizedExperiment'
makeTreeSEFromPhyloseq
                        Coerce a 'phyloseq' object to a
                        'TreeSummarizedExperiment'
meltAssay               Converting a 'SummarizedExperiment' object into
                        a long data.frame
merge-methods           Merge a subset of the rows or columns of a
                        'SummarizedExperiment'
mergeSEs                Merge SE objects into single SE object.
mia-datasets            mia datasets
mia-package             'mia' Package.
perSampleDominantTaxa   Get dominant taxa
relabundance            Getter / setter for relative abundance data
runCCA                  Canonical Correspondence Analysis
runDPCoA                Calculation of Double Principal Correspondance
                        analysis
runNMDS                 Perform non-metric MDS on sample-level data
splitByRanks            Split/Unsplit a 'SingleCellExperiment' by
                        taxonomic ranks
splitOn                 Split 'TreeSummarizedExperiment' column-wise or
                        row-wise based on grouping variable
subsampleCounts         Subsample Counts
subsetSamples           Subset functions
summaries               Summarizing microbiome data
taxonomy-methods        Functions for accessing taxonomic data stored
                        in 'rowData'.
transformCounts         Transform Counts
