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MicrobiomeBenchmarkData

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

Datasets for benchmarking in microbiome research


Bioconductor version: Development (3.19)

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] , Levi Waldron [aut] , Marcel Ramos [ctb]

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

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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

Details

biocViews ExperimentData, MicrobiomeData, ReproducibleResearch, SequencingData
Version 1.5.0
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
See More
Suggests rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0), mia, ggplot2, tidyr, dplyr, magrittr, tibble, purrr
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Package Archives

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

Source Package MicrobiomeBenchmarkData_1.5.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (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/
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