Obtain the Silverman Artificial Gut data

Obtain the microbiome data from Silverman et al. (2018).

SilvermanAGutData()

artificialgut()

Value

a TreeSummarizedExperiment

Details

The SilvermanAGutData dataset contains 16S rRNA gene based high-throughput profiling of 4 in vitro artificial gut models. The sampling was done hourly and daily to capture sub-daily dynamics of microbial community originating from human feces. The data consists of 413 taxa from 639 samples. The data set can be used to investigate longitudinal dynamics of microbial community in a controlled environment.

Column metadata includes the days of sampling, vessel identifier, sampling frequency pre-post challenge with Bacteroides ovatus.

The wow metadata of the microbiome data contains taxonomic information on the Kingdom, Phylum, Class, Order, Family and Genus and Species level.

The row tree consists of a phylogenetic tree build using sequence information of 413 taxa.

As reference sequences the ASV are provided.

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

References

Silveman J.D et al. (2018): Dynamic linear models guide design and analysis of microbiota studies within artificial human guts. Microbiome 6:202 https://doi.org/10.1186/s40168-018-0584-3

Author

Sudarshan A. Shetty and Felix G.M. Ernst

Examples

tse <- SilvermanAGutData()
#> Warning: SilvermanAGutData has been moved to the miaTime package. The microbiomeDataSets::SilvermanAGutData will be deprecated soon.
#> 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
#> see ?microbiomeDataSets and browseVignettes('microbiomeDataSets') for documentation
#> loading from cache