MicrobiomeBenchmarkData
This is the development version of MicrobiomeBenchmarkData; for the stable release version, see MicrobiomeBenchmarkData.
Datasets for benchmarking in microbiome research
Bioconductor version: Development (3.21)
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:
Maintainer: Samuel Gamboa <Samuel.Gamboa.Tuz at gmail.com>
citation("MicrobiomeBenchmarkData")):
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("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 | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, MicrobiomeData, ReproducibleResearch, SequencingData |
| Version | 1.9.0 |
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | bugphyzz |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MicrobiomeBenchmarkData_1.9.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/MicrobiomeBenchmarkData |
| Source Repository (Developer Access) | git clone [email protected]:packages/MicrobiomeBenchmarkData |
| Package Short Url | https://bioconductor.org/packages/MicrobiomeBenchmarkData/ |
| Package Downloads Report | Download Stats |