HMP2Data

DOI: 10.18129/B9.bioc.HMP2Data    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see HMP2Data.

16s rRNA sequencing data from the Human Microbiome Project 2

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	HMP2Data
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ExperimentData, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch, SequencingData
Version	1.4.0
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
LinkingTo
Suggests	Biobase, BiocCheck, BiocManager, BiocStyle, cowplot, devtools, ggplot2, gridExtra, haven, rmarkdown, roxygen2, stats, testthat, tibble, UpSetR
SystemRequirements
Enhances
URL	https://github.com/jstansfield0/HMP2Data
BugReports	https://github.com/jstansfield0/HMP2Data/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	HMP2Data_1.4.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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/
Package Downloads Report	Download Stats