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Bioconductor - HMP2Data

HMP2Data

This is the released version of HMP2Data; for the devel version, see HMP2Data.

16s rRNA sequencing data from the Human Microbiome Project 2

Bioconductor version: Release (3.21)

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 vcu.edu>, Ekaterina Smirnova <ekaterina.smirnova at vcuhealth.org>, Ni Zhao <nzhao10 at jhu.edu>, Jennifer Fettweis <jennifer.fettweis at vcuhealth.org>, Levi Waldron <levi.waldron at sph.cuny.edu>, Mikhail Dozmorov <mikhail.dozmorov at vcuhealth.org>

Maintainer: John Stansfield <stansfieldjc at vcu.edu>, Ekaterina Smirnova <ekaterina.smirnova at vcuhealth.org>

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

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("HMP2Data")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("HMP2Data")
Details biocViews ExperimentData, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch, SequencingData Version 1.22.0 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 System Requirements URL https://github.com/jstansfield0/HMP2Data Bug Reports https://github.com/jstansfield0/HMP2Data/issues See More Suggests Biobase, BiocCheck, BiocManager, BiocStyle, cowplot, devtools, ggplot2, gridExtra, haven, rmarkdown, roxygen2, stats, testthat, tibble, UpSetR Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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