collapse = TRUE,
    comment = "#>"

Microbiome example data sets

The data sets are primarily named by the first author of the associated publication, together with a descriptive suffix. Aliases are provided for some of the data sets.

A table of the available data sets is available through the availableDataSets function.


All data are downloaded from ExperimentHub and cached for local re-use. Check the man pages of each function for a detailed documentation of the data contents and original source.

The microbiome data is usually loaded as a r Biocpkg("TreeSummarizedExperiment"). If other associated data tables (metabolomic, biomarker..) are provided, the integrated data collection is provided as r Biocpkg("MultiAssayExperiment").

For more information on how to use these objects, please refer to the vignettes of those packages.


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