HMP16SData

DOI: 10.18129/B9.bioc.HMP16SData    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see HMP16SData.

16S rRNA Sequencing Data from the Human Microbiome Project

Bioconductor version: 3.12

HMP16SData is a Bioconductor ExperimentData package of the Human Microbiome Project (HMP) 16S rRNA sequencing data for variable regions 1–3 and 3–5. Raw data files are provided in the package as downloaded from the HMP Data Analysis and Coordination Center. Processed data is provided as SummarizedExperiment class objects via ExperimentHub.

Author: Lucas Schiffer <schiffer.lucas at gmail.com>, Rimsha Azhar <rimsha_azhar at hotmail.com>, Marcel Ramos <marcel.ramos at roswellpark.org>, Ludwig Geistlinger <ludwig.geistlinger at sph.cuny.edu>, Levi Waldron <lwaldron.research at gmail.com>

Maintainer: Lucas Schiffer <schiffer.lucas at gmail.com>

Installation

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

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

BiocManager::install("HMP16SData")

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("HMP16SData")

 

HTML	R Script	HMP16SData
PDF		Reference Manual
Text		NEWS

Details

biocViews	ExperimentData, ExperimentHub, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch, SequencingData
Version	1.10.0
License	Artistic-2.0
Depends	R (>= 4.0.0), SummarizedExperiment
Imports	AnnotationHub, assertthat, dplyr, ExperimentHub, kableExtra, knitr, magrittr, methods, readr, S4Vectors, stringr, tibble, utils
LinkingTo
Suggests	Biobase, BiocCheck, BiocManager, BiocStyle, circlize, covr, cowplot, curatedMetagenomicData, dendextend, devtools, ggplot2, gridExtra, haven, phyloseq, rmarkdown, roxygen2, stats, testthat
SystemRequirements
Enhances
URL	https://github.com/waldronlab/HMP16SData
BugReports	https://github.com/waldronlab/HMP16SData/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	HMP16SData_1.10.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/HMP16SData
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HMP16SData
Package Short Url	https://bioconductor.org/packages/HMP16SData/
Package Downloads Report	Download Stats