GlobalPatterns          Global patterns of 16S rRNA diversity at a
                        depth of millions of sequences per sample.
HintikkaXOData          Multiomics dataset from 40 rat samples
Tengeler2020            Gut microbiota profiles of 27 individuals with
                        ADHD and healthy controls
Tito2024QMP             Fecal microbiota samples from 589 patients
                        across different colorectal cancer stages
addAlpha                Estimate alpha diversity indices
addCluster              Clustering wrapper
addContaminantQC        decontam functions
addDissimilarity        Calculate dissimilarities
addDivergence           Estimate divergence
addMediation            Perform mediation analysis
agglomerateByPrevalence
                        Agglomerate data based on population prevalence
agglomerateByRank       Agglomerate data using taxonomic information or
                        other grouping
calculateDMN            Dirichlet-Multinomial Mixture Model: Machine
                        Learning for Microbiome Data
convertFromDADA2        Create a 'TreeSummarizedExperiment' object from
                        'DADA2' results
convertToBIOM           Convert a 'TreeSummarizedExperiment' object
                        to/from 'BIOM' results
convertToPhyloseq       Create a 'TreeSummarizedExperiment' object from
                        a phyloseq object
deprecate               These functions will be deprecated. Please use
                        other functions instead.
dmn_se                  Twins' microbiome data from 278 individuals
enterotype              Human gut microbiome dataset from 22 subjects
                        based on shotgun DNA sequencing
esophagus               Human esophageal community from 3 individuals
getAbundant             Determine abundant and rare taxa. Rare taxa can
                        be further classified to conditionally rare and
                        permanently rare.
getCCA                  Canonical Correspondence Analysis and
                        Redundancy Analysis
getCrossAssociation     Calculate correlations between features of two
                        experiments.
getDPCoA                Calculation of Double Principal Correspondance
                        analysis
getDominant             Get dominant taxa
getHierarchyTree        Calculate hierarchy tree
getLDA                  Latent Dirichlet Allocation
getMDS                  Perform multi-dimensional scaling (MDS)
getNMDS                 Perform non-metric MDS on sample-level data
getNMF                  Non-negative Matrix Factorization
getPERMANOVA            Calculate PERMANOVA (Permutational Multivariate
                        Analysis of Variance)
getPrevalence           Calculation prevalence information for features
                        across samples
getReducedDimAttribute
                        Utilization functions for
                        'TreeSummarizedExperiment' objects
importHUMAnN            Import HUMAnN results to
                        'TreeSummarizedExperiment'
importMetaPhlAn         Import Metaphlan results to
                        'TreeSummarizedExperiment'
importMothur            Import Mothur results as a
                        'TreeSummarizedExperiment'
importQIIME2            Import QIIME2 results to
                        'TreeSummarizedExperiment'
importTaxpasta          Import taxpasta-specific BIOM results to
                        'TreeSummarizedExperiment'
meltSE                  Converting a 'SummarizedExperiment' object into
                        a long data.frame
mergeSEs                Merge SE objects into single SE object.
mia-datasets            mia datasets
mia-package             'mia' Package.
peerj13075              Skin microbial profiles 58 genetically
                        unrelated individuals
rarefyAssay             Subsample Counts
splitOn                 Split 'TreeSummarizedExperiment' column-wise or
                        row-wise based on grouping variable
summarizeDominance      Summarizing microbiome data
taxonomyRanks           Functions for accessing taxonomic data stored
                        in 'rowData'.
transformAssay          Transform assay
