microbiomeDataSets

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

Experiment Hub based microbiome datasets

Bioconductor version: Development (3.21)

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] (ORCID: ), Felix G.M. Ernst [aut] (ORCID: ), Sudarshan Shetty [aut] (ORCID: ), Chouaib Benchraka [ctb] (ORCID: ), 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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, ExperimentHub, MicrobiomeData, SequencingData
Version	1.15.0
License	CC0
Depends	R (>= 4.1), SummarizedExperiment, TreeSummarizedExperiment, MultiAssayExperiment
Imports	methods, utils, BiocGenerics, ExperimentHub, Biostrings, ape
System Requirements
URL

Suggests	knitr, rmarkdown, BiocStyle, SingleCellExperiment, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	mia
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	microbiomeDataSets_1.15.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/microbiomeDataSets
Source Repository (Developer Access)	git clone [email protected]:packages/microbiomeDataSets
Package Short Url	https://bioconductor.org/packages/microbiomeDataSets/
Package Downloads Report	Download Stats