MicrobiomeBenchmarkData

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16

Datasets for benchmarking in microbiome research

Bioconductor version: Development (3.24)

The MicrobiomeBenchmarkData package provides functionality to access microbiome datasets suitable for benchmarking. These datasets have some biological truth, which allows to have expected results for comparison. The datasets come from various published sources and are provided as TreeSummarizedExperiment objects. Currently, only datasets suitable for benchmarking differential abundance methods are available.

Author: Samuel Gamboa [aut, cre] ORCID: 0000-0002-6863-7943 , Levi Waldron [aut] ORCID: 0000-0003-2725-0694 , Marcel Ramos [ctb], NCI [fnd] (GrantNo.: R01CA230551)

Maintainer: Samuel Gamboa <Samuel.Gamboa.Tuz at gmail.com>

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

Samuel Gamboa, Levi Waldron. MicrobiomeBenchmarkData: Datasets for benchmarking in microbiome research. doi:10.18129/B9.bioc.MicrobiomeBenchmarkData, R package version 1.15.1, https://bioconductor.org/packages/MicrobiomeBenchmarkData.

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")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("MicrobiomeBenchmarkData")

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("MicrobiomeBenchmarkData")

Datasets in MicrobiomeBenchmarkData	HTML	R Script
MicrobiomeBenchmarkData	HTML	R Script
Recalibration of the Stammler_2016_16S_spikein dataset	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, MicrobiomeData, ReproducibleResearch, SequencingData
Version	1.15.1
In Bioconductor since	BioC 3.16 (R-4.2) (4 years)
License	Artistic-2.0
Depends	R (>= 4.2), SummarizedExperiment, TreeSummarizedExperiment
Imports	BiocFileCache, tools, S4Vectors, ape, utils
System Requirements
URL	https://github.com/waldronlab/MicrobiomeBenchmarkData http://waldronlab.io/MicrobiomeBenchmarkData/
Bug Reports	https://github.com/waldronlab/MicrobiomeBenchmarkData/issues

Suggests	rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0), mia, ggplot2, tidyr, dplyr, magrittr, tibble, purrr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	bugphyzz
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	MicrobiomeBenchmarkData_1.15.1.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/MicrobiomeBenchmarkData
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MicrobiomeBenchmarkData
Package Short Url	https://bioconductor.org/packages/MicrobiomeBenchmarkData/
Package Downloads Report	Download Stats