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This is the development version of HMP2Data; for the stable release version, see HMP2Data.

16s rRNA sequencing data from the Human Microbiome Project 2

Bioconductor version: Development (3.20)

HMP2Data is a Bioconductor package of the Human Microbiome Project 2 (HMP2) 16S rRNA sequencing data. Processed data is provided as phyloseq, SummarizedExperiment, and MultiAssayExperiment class objects. Individual matrices and data.frames used for building these S4 class objects are also provided in the package.

Author: John Stansfield <stansfieldjc at>, Ekaterina Smirnova <ekaterina.smirnova at>, Ni Zhao <nzhao10 at>, Jennifer Fettweis <jennifer.fettweis at>, Levi Waldron <levi.waldron at>, Mikhail Dozmorov <mikhail.dozmorov at>

Maintainer: John Stansfield <stansfieldjc at>, Ekaterina Smirnova <ekaterina.smirnova at>

Citation (from within R, enter citation("HMP2Data")):


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

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

# The following initializes usage of Bioc devel


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:

HMP2Data HTML R Script
Reference Manual PDF


biocViews ExperimentData, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch, SequencingData
Version 1.19.0
License Artistic-2.0
Depends R (>= 3.6.0)
Imports AnnotationHub, assertthat, dplyr, ExperimentHub, kableExtra, knitr, magrittr, methods, readr, S4Vectors, SummarizedExperiment, phyloseq, MultiAssayExperiment, data.table
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Suggests Biobase, BiocCheck, BiocManager, BiocStyle, cowplot, devtools, ggplot2, gridExtra, haven, rmarkdown, roxygen2, stats, testthat, tibble, UpSetR
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Follow Installation instructions to use this package in your R session.

Source Package HMP2Data_1.19.0.tar.gz
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