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HMP16SData

16S rRNA Sequencing Data from the Human Microbiome Project


Bioconductor version: Release (3.18)

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] , 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 "4.3") 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

Details

biocViews ExperimentData, ExperimentHub, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch, SequencingData
Version 1.22.0
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
See More
Suggests Biobase, BiocCheck, BiocManager, BiocStyle, circlize, cowplot, dendextend, devtools, ggplot2, gridExtra, haven, phyloseq, rmarkdown, roxygen2, stats, testthat, tidyr
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Package Archives

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

Source Package HMP16SData_1.22.0.tar.gz
Windows Binary
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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