Datasets in MicrobiomeBenchmarkData

In the table below, you can find the collection of datasets currently available through the MicrobiomeBenchmarkData package. These datasets are also avialable on Zenodo: https://doi.org/10.5281/zenodo.6911026

Dataset Dimensions Body site Contrasts Biological ground truth PMID
HMP_2012_16S_gingival_V13 33127 x 311 Gingiva Subgingival vs Supragingival plaque. Enrichment of aerobic taxa in the supragingival plaque and enrichment of anaerobic taxa in the subgingival plaque. 22699609
HMP_2012_16S_gingival_V35 17949 x 311 Gingiva Subgingival vs Supragingival plaque. Enrichment of aerobic taxa in the supragingival plaque and enrichment of anaerobic taxa in the subgingival plaque. 22699609
HMP_2012_16S_gingival_V35_subset 892 x 76 Gingiva Subgingival vs Supragingival plaque. Enrichment of aerobic taxa in the supragingival plaque and enrichment of anaerobic taxa in the subgingival plaque. 22699609
HMP_2012_WMS_gingival 235 x 16 Gingiva Subgingival vs Supragingival plaque. Enrichment of aerobic taxa in the supragingival plaque and enrichment of anaerobic taxa in the subgingival plaque. 22699609
Stammler_2016_16S_spikein 247 x 394 Stool Pre-ASCT (allogeneic stem cell transplantation) vs 14 days after treatment. Same bacterial loads of the spike-in bacteria across all samples: Salinibacter ruber (extreme halophilic), Rhizobium radiobacter (found in soils and plants), and Alicyclobacillus acidiphilu (thermo-acidophilic). 27329048
Ravel_2011_16S_BV 4036 x 17 Vagina Healthy vs bacterial vaginosis Decrease of Lactobacillus and increase of bacteria isolated during bacterial vaginosis in samples with high Nugent scores (bacterial vaginosis). 20534435