Obtain the Song quality assurance dataset

Obtain the microbiome data from Song et al. (2016).

SongQAData()

qa10934()

Source

https://qiita.ucsd.edu/study/description/10394

Value

a TreeSummarizedExperiment

Details

The SongQA dataset contains microbiome data from a study comparing different sample preparation methods focusing on temperature and DNA extraction methods mainly.

The dataset was generated by sequencing the variable region 4 of 16S rRNA genes via Illumina HiSeq or MiSeq.

Column metadata was reconstructed from sample names and includes information on the source, timepoint, extraction method, temperature conditions and other optional data.

Row metadata contains taxonomic information on the Phylum, Family and Genus level.

All data are downloaded from ExperimentHub and cached for local re-use.

References

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies. Se Jin Song, Amnon Amir, Jessica L. Metcalf, Katherine R. Amato, Zhenjiang Zech Xu, Greg Humphrey, Rob Knight. mSystems May 2016, 1 (3) e00021-16; DOI: 10.1128/mSystems.00021-16

Author

Felix G.M. Ernst

Examples

tse <- SongQAData()
#> see ?microbiomeDataSets and browseVignettes('microbiomeDataSets') for documentation
#> loading from cache
#> see ?microbiomeDataSets and browseVignettes('microbiomeDataSets') for documentation
#> loading from cache
#> see ?microbiomeDataSets and browseVignettes('microbiomeDataSets') for documentation
#> loading from cache
#> see ?microbiomeDataSets and browseVignettes('microbiomeDataSets') for documentation
#> loading from cache