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HMP2Data

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 (3.18)

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 "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews ExperimentData, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch, SequencingData
Version 1.15.0
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
Linking To
Suggests Biobase, BiocCheck, BiocManager, BiocStyle, cowplot, devtools, ggplot2, gridExtra, haven, rmarkdown, roxygen2, stats, testthat, tibble, UpSetR
System Requirements
Enhances
URL https://github.com/jstansfield0/HMP2Data
Bug Reports https://github.com/jstansfield0/HMP2Data/issues
See More
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_1.15.0.tar.gz
Windows Binary
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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