HMP16SData

This is the released version of HMP16SData; for the devel version, see HMP16SData.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

16S rRNA Sequencing Data from the Human Microbiome Project

Bioconductor version: Release (3.23)

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 [aut, cre] ORCID: 0000-0003-3628-0326 , Rimsha Azhar [aut], Marcel Ramos [ctb], Ludwig Geistlinger [ctb], Levi Waldron [aut]

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

Citation (from within R, enter citation("HMP16SData")):

Lucas schiffer, Rimsha Azhar, Levi Waldron. HMP16SData: 16S rRNA Sequencing Data from the Human Microbiome Project. doi:10.18129/B9.bioc.HMP16SData, R package version 1.32.0, https://bioconductor.org/packages/HMP16SData.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("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")

HMP16SData	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, ExperimentHub, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch, SequencingData
Version	1.32.0
In Bioconductor since	BioC 3.7 (R-3.5) (8.5 years)
License	Artistic-2.0
Depends	R (>= 4.1.0), SummarizedExperiment
Imports	AnnotationHub, ExperimentHub, S4Vectors, assertthat, dplyr, kableExtra, knitr, magrittr, methods, readr, stringr, tibble, utils
System Requirements
URL	https://github.com/waldronlab/HMP16SData
Bug Reports	https://github.com/waldronlab/HMP16SData/issues

Suggests	Biobase, BiocCheck, BiocManager, BiocStyle, circlize, cowplot, dendextend, devtools, ggplot2, gridExtra, haven, phyloseq, rmarkdown, roxygen2, stats, testthat, tidyr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	HMP16SData_1.32.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
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