Prepare data for MicrobiomeBenchmarkData

Files

• Data files uploaded to Zenodo are in the data directory.
• Other files that were necessary are in the other_data directory.
• Scripts for generating the files in both data and other_data are stored in the scripts directory.

Datasets components

Dataset	count matrix	sample metadata	taxonomy table	taxa annotations	phylogenetic tree
HMP_2012_16S_gingival_V13	yes	yes	yes	yes	yes
HMP_2012_16S_gingival_V35	yes	yes	yes	yes	yes
HMP_2012_16S_gingival_V35_subset	yes	yes	yes	yes	yes
HMP_2012_WMS_gingival	yes	yes	yes	yes	yes
Stammler_2016_16S_spikein	yes	yes	yes
Ravel_2011_16S_BV	yes	yes	yes	yes

General instructions

1. Update output files (those in the data directory).
2. If sample metadata files where modified, run the sampleMetadata.R script as well.
3. After commit and push, upload files to Zenodo.
4. Go to the MicrobiomeBenchmarkData repo and update sampleMetadata and sysdata.

Links

• Data on Zenodo: https://zenodo.org/record/6911027
• 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