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microbiomeDataSets

This is the development version of microbiomeDataSets; for the stable release version, see microbiomeDataSets.

Experiment Hub based microbiome datasets

Bioconductor version: Development (3.18)

microbiomeDataSets is a collection of microbiome datasets loaded from Bioconductor'S ExperimentHub infrastructure. The datasets serve as reference for workflows and vignettes published adjacent to the microbiome analysis tools on Bioconductor. Additional datasets can be added overtime and additions from authors are welcome.

Author: Leo Lahti [cre, aut] , Felix G.M. Ernst [aut] , Sudarshan Shetty [aut] , Chouaib Benchraka [ctb] , Yagmur Simsek [ctb]

Maintainer: Leo Lahti <leo.lahti at iki.fi>

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

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("microbiomeDataSets")

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("microbiomeDataSets")
microbiomeDataSets HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ExperimentData, ExperimentHub, MicrobiomeData, SequencingData
Version 1.9.0
License CC0
Depends R (>= 4.1), SummarizedExperiment, TreeSummarizedExperiment, MultiAssayExperiment
Imports methods, utils, BiocGenerics, ExperimentHub, Biostrings, ape
Linking To
Suggests knitr, rmarkdown, BiocStyle, SingleCellExperiment, testthat
System Requirements
Enhances
URL
See More
Depends On Me
Imports Me
Suggests Me mia, miaViz
Links To Me
Build Report  

Package Archives

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

Source Package microbiomeDataSets_1.9.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/microbiomeDataSets
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/microbiomeDataSets
Package Short Url https://bioconductor.org/packages/microbiomeDataSets/
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