MicrobiomeBenchmarkData

DOI: 10.18129/B9.bioc.MicrobiomeBenchmarkData    

Datasets for benchmarking in microbiome research

Bioconductor version: Release (3.16)

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 "4.2") and enter:

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

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")

 

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

Details

biocViews ExperimentData, MicrobiomeData, ReproducibleResearch, SequencingData
Version 1.0.0
License Artistic-2.0
Depends R (>= 4.2), SummarizedExperiment, TreeSummarizedExperiment
Imports BiocFileCache, tools, S4Vectors, ape, utils
LinkingTo
Suggests rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0), mia, ggplot2, tidyr, dplyr, magrittr, tibble, purrr
SystemRequirements
Enhances
URL https://github.com/waldronlab/MicrobiomeBenchmarkData http://waldronlab.io/MicrobiomeBenchmarkData/
BugReports https://github.com/waldronlab/MicrobiomeBenchmarkData/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package MicrobiomeBenchmarkData_1.0.0.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/
Package Downloads Report Download Stats

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