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Experiment Hub based microbiome datasets

Bioconductor version: Release (3.19)

microbiomeDataSets is a collection of microbiome datasets loaded from Bioconductor'S ExperimentHub infrastructure. The datasets serve as reference for workflows and vignettes published adjacent to the microbiome analysis tools on Bioconductor. Additional datasets can be added overtime and additions from authors are welcome.

Author: Leo Lahti [cre, aut] , Felix G.M. Ernst [aut] , Sudarshan Shetty [aut] , Chouaib Benchraka [ctb] , Yagmur Simsek [ctb]

Maintainer: Leo Lahti <leo.lahti at>

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


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

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


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:

microbiomeDataSets HTML R Script
Reference Manual PDF


biocViews ExperimentData, ExperimentHub, MicrobiomeData, SequencingData
Version 1.12.1
License CC0
Depends R (>= 4.1), SummarizedExperiment, TreeSummarizedExperiment, MultiAssayExperiment
Imports methods, utils, BiocGenerics, ExperimentHub, Biostrings, ape
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Suggests knitr, rmarkdown, BiocStyle, SingleCellExperiment, testthat
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Imports Me
Suggests Me mia, miaViz
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Follow Installation instructions to use this package in your R session.

Source Package microbiomeDataSets_1.12.1.tar.gz
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