vignettes/datasets.Rmd
datasets.RmdIn 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 |