HMP2Data

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see HMP2Data.

16s rRNA sequencing data from the Human Microbiome Project 2

Bioconductor version: 3.19

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 "4.4") 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")

HMP2Data HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ExperimentData, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch, SequencingData

Version 1.18.0

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

Suggests Biobase, BiocCheck, BiocManager, BiocStyle, cowplot, devtools, ggplot2, gridExtra, haven, rmarkdown, roxygen2, stats, testthat, tibble, UpSetR

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Package Archives

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

Source Package HMP2Data_1.18.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

Source Repository git clone https://git.bioconductor.org/packages/HMP2Data

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HMP2Data

Package Short Url https://bioconductor.org/packages/HMP2Data/

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