HMP16SData

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

16S rRNA Sequencing Data from the Human Microbiome Project

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DOI: 10.18129/B9.bioc.HMP16SData

Bioconductor version: Release (3.22)

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 iD 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")):

Installation

To install this package, start R (version "4.5") 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 1.30.0

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

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

Source Package HMP16SData_1.30.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (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/

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