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This is the development version of mia; for the stable release version, see mia.

Microbiome analysis

Bioconductor version: Development (3.20)

mia implements tools for microbiome analysis based on the SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment infrastructure. Data wrangling and analysis in the context of taxonomic data is the main scope. Additional functions for common task are implemented such as community indices calculation and summarization.

Author: Felix G.M. Ernst [aut] , Sudarshan A. Shetty [aut] , Tuomas Borman [aut, cre] , Leo Lahti [aut] , Yang Cao [ctb], Nathan D. Olson [ctb], Levi Waldron [ctb], Marcel Ramos [ctb], H├ęctor Corrada Bravo [ctb], Jayaram Kancherla [ctb], Domenick Braccia [ctb], Basil Courbayre [ctb], Muluh Muluh [ctb], Giulio Benedetti [ctb], Moritz Emanuel Beber [ctb]

Maintainer: Tuomas Borman <tuomas.v.borman at>

Citation (from within R, enter citation("mia")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

mia HTML R Script
Reference Manual PDF


biocViews DataImport, Microbiome, Software
Version 1.13.27
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License Artistic-2.0 | file LICENSE
Depends R (>= 4.0), SummarizedExperiment, SingleCellExperiment, TreeSummarizedExperiment(>= 1.99.3), MultiAssayExperiment
Imports methods, stats, utils, MASS, ape, decontam, vegan, BiocGenerics, S4Vectors, IRanges, Biostrings, DECIPHER, BiocParallel, DelayedArray, DelayedMatrixStats, scuttle, scater, DirichletMultinomial, rlang, dplyr, tibble, tidyr, bluster, MatrixGenerics, mediation, rbiom
System Requirements
Bug Reports
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Suggests testthat, knitr, patchwork, BiocStyle, yaml, phyloseq, dada2, stringr, biomformat, reldist, ade4, microbiomeDataSets, rmarkdown, rhdf5
Linking To
Depends On Me miaViz
Imports Me ANCOMBC, dar, MGnifyR, curatedMetagenomicData
Suggests Me CBEA, miaSim, philr, MicrobiomeBenchmarkData, MiscMetabar
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package mia_1.13.27.tar.gz
Windows Binary
macOS Binary (x86_64) mia_1.13.27.tgz
macOS Binary (arm64) mia_1.13.23.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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