This report contains benchmarking results for the transform operation with common microbiome data containers in R/Bioconductor for the transform operation.
The tests utilize the following publicly available data sets. We thank the original authors for making these valuable data resources openly available. Check the links for details and original references:
- SongQAData Song et al. (2016)
- HMP_2019_ibdmdb (source 1, source 2)
- ShaoY_2019
Full sample sizes by data set:
| Dataset | N |
|---|---|
| SongQAData | 1522 |
| HMP_2019_ibdmdb | 1627 |
| ShaoY_2019 | 1644 |
Feature counts by data set:
| Rank | SongQAData | HMP_2019_ibdmdb | ShaoY_2019 |
|---|---|---|---|
| Phylum | 39 | 15 | 14 |
| Family | 271 | 69 | 90 |
| Species | 374 | 579 | 819 |
