Analyses using MicrobiomeBenchmarkData

This package contains analyses performed on datasets included or under consideration to be included in the MicrobiomeBenchmarkData package, which provides benchmark datasets for differential abundance methods in microbiome research.

Package website: https://waldronlab.io/MicrobiomeBenchmarkDataAnalyses

Installation

## Package installation
if (!"BiocManager" %in% install.packages()[,"Package"])
  install.packages("BiocManager")
BiocManager::install("waldronlab/MicrobiomeBenchmarkDataAnalyses")

Links

• Data on Zenodo: https://zenodo.org/record/6911027
• R package on Bioconductor: https://www.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

TODO

• Create a custom function for plotting enrichment and positives.