HMP2Data

16s rRNA sequencing data from the Human Microbiome Project 2

Bioconductor version: Release (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
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.

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/
Package Downloads Report	Download Stats