This R package is a collection of microbiome datasets published initially elsewhere. The data is available as TreeSummarizedExperiment or MultiAssayExperiment and a list of available dataset can be retrieved via the availableDataSets() function.

The microbiomeDataSets package focuses mainly on non-human studies. The independent curatedMetagenomicData package provides access to a large collection of standardized human microbiome studies in the same format.

The aim is to provide datasets for teaching, example workflows or comparative efforts. If you have a dataset, which you like to see in this package, please let us know and/or provide a PR for the datasets.


Feel free to contribute. Have a look at how existing datasets are organized and prepared data accordingly. It is also good to get in touch at the earliest convenience to discuss any issues.

Technical aspects

Let's use a gitflow approach. Development version should be done against the master branch and then merged to master for the next release. (

Resources on how data is added to Bioconductor's ExperimentHub backend and accessed are available from Bioconductor ExperimentHub documentation and in Creating ExperimentHub Package.

Basic steps:

Code of conduct

Please note that the microbiomeDataSets project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

microbiome/microbiomeDataSets documentation built on July 31, 2022, 6:09 a.m.