Gingival data set from the Human Microbiome Project

Usage

data(hmp_gingival)

Format

A list with two elements

data: The microbiome relative abundance data with relevant metadata obtained from the Human Microbiome Project via the HMP16SData package (snapshot: 11-15-2021). The data set is hosted the container of type phyloseq. Using the mia package users can convert it to the TreeSummarizedExperiment type.
set: Sets of microbes based on their metabolism annotation at the Genera level. Annotations obtained via Calagaro et al.'s repository on Zenodo (https://doi.org/10.5281/zenodo.3942108)

References

Data can be downloaded directly from https://hmpdacc.org/hmp/

R interface of the data from https://doi.org/doi:10.18129/B9.bioc.HMP16SData

Beghini F, Renson A, Zolnik CP, Geistlinger L, Usyk M, Moody TU, et al. Tobacco Exposure Associated with Oral Microbiota Oxygen Utilization in the New York City Health and Nutrition Examination Study. Annals of Epidemiology. 2019;34:18–25.e3. doi:10.1016/j.annepidem.2019.03.005

Consortium THMP, Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, et al. Structure, Function and Diversity of the Healthy Human Microbiome. Nature. 2012;486(7402):207–214. doi:10.1038/nature11234.

Calgaro M, Romualdi C, Waldron L, Risso D, Vitulo N. Assessment of Statistical Methods from Single Cell, Bulk RNA-Seq, and Metagenomics Applied to Microbiome Data. Genome Biology. 2020;21(1):191. doi:10.1186/s13059-020-02104-1

Schiffer L, Azhar R, Shepherd L, Ramos M, Geistlinger L, Huttenhower C, et al. HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor. American Journal of Epidemiology. 2019;doi:10.1093/aje/kwz006.