DOI: 10.18129/B9.bioc.MicrobiomeBenchmarkData  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see MicrobiomeBenchmarkData.

Datasets for benchmarking in microbiome research

Bioconductor version: 3.17

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")):


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


biocViews ExperimentData, MicrobiomeData, ReproducibleResearch, SequencingData
Version 1.2.0
License Artistic-2.0
Depends R (>= 4.2), SummarizedExperiment, TreeSummarizedExperiment
Imports BiocFileCache, tools, S4Vectors, ape, utils
Suggests rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0), mia, ggplot2, tidyr, dplyr, magrittr, tibble, purrr
URL https://github.com/waldronlab/MicrobiomeBenchmarkData http://waldronlab.io/MicrobiomeBenchmarkData/
BugReports https://github.com/waldronlab/MicrobiomeBenchmarkData/issues
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Source Package MicrobiomeBenchmarkData_1.2.0.tar.gz
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Package Short Url https://bioconductor.org/packages/MicrobiomeBenchmarkData/
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