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Datasets for benchmarking in microbiome research

Bioconductor version: Release (3.19)

The MicrobiomeBenchmarkData package provides functionality to access microbiome datasets suitable for benchmarking. These datasets have some biological truth, which allows to have expected results for comparison. The datasets come from various published sources and are provided as TreeSummarizedExperiment objects. Currently, only datasets suitable for benchmarking differential abundance methods are available.

Author: Samuel Gamboa [aut, cre] , Levi Waldron [aut] , Marcel Ramos [ctb]

Maintainer: Samuel Gamboa <Samuel.Gamboa.Tuz at>

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


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:

Datasets in MicrobiomeBenchmarkData HTML R Script
MicrobiomeBenchmarkData HTML R Script
Recalibration of the Stammler_2016_16S_spikein dataset HTML R Script
Reference Manual PDF


biocViews ExperimentData, MicrobiomeData, ReproducibleResearch, SequencingData
Version 1.6.0
License Artistic-2.0
Depends R (>= 4.2), SummarizedExperiment, TreeSummarizedExperiment
Imports BiocFileCache, tools, S4Vectors, ape, utils
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Suggests rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0), mia, ggplot2, tidyr, dplyr, magrittr, tibble, purrr
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Follow Installation instructions to use this package in your R session.

Source Package MicrobiomeBenchmarkData_1.6.0.tar.gz
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