waldronlab / MicrobiomeBenchmarkData

Data for benchmarking in microbiome research.

MicrobiomeBenchmarkData

Access to a resource of datasets with biological ground truth for benchmarking differential abundance methods. The datasets are available from Zenodo: https://doi.org/10.5281/zenodo.6911026

Installation

## Install BioConductor if not installed
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## Release version (not yet in Bioc)
BiocManager::install("MicrobiomeBenchmarkData")

## Development version
BiocManager::install("waldronlab/MicrobiomeBenchmarkData", build_vignettes = TRUE)

Links

• Data on Zenodo: https://doi.org/10.5281/zenodo.6911026
• R package on Bioconductor: https://bioconductor.org/packages/release/data/experiment/html/MicrobiomeBenchmarkData.html
• R package source code: https://github.com/waldronlab/MicrobiomeBenchmarkData
• R package issues: https://github.com/waldronlab/MicrobiomeBenchmarkData/issues
• Scripts for preparing the datasets: https://github.com/waldronlab/MicrobiomeBenchmarkDataPrep
• Code for reproducibility of the analyses: https://waldronlab.io/MicrobiomeBenchmarkDataAnalyses