SprockettTHData.RdObtain the microbiome data from Sprockett et al. (2020).
SprockettTHData()a TreeSummarizedExperiment
The SprockettTHData dataset contains 16S rRNA gene based high-throughput profiling of 1966 Feces, 120 Saliva samples from 319 participants from Bolivia, Finland and Bangladesh. These include samples from adults, children, and infants. Several participants have longitudinal samples. The data consists of 2319 taxa from 2086 samples. The data set can be used to investigate assembly, structure, and dynamics as well as associations between several host related parameters with microbiota.
Column metadata includes the sex, age, feeding status, delivery mode, country, and other information.
The row metadata of the microbiome data contains taxonomic information on the Kingdom, Phylum, Class, Order, Family and Genus, Species and lowest taxonomic rank.
The row tree consists of a phylogenetic tree build using sequence information of 2319 taxa.
As reference sequences the ASV are provided.
All data are downloaded from ExperimentHub and cached for local re-use.
Sprockett, D.D., Martin, M., Costello, E.K. et al. (2020) Microbiota assembly, structure, and dynamics among Tsimane horticulturalists of the Bolivian Amazon. Nat Commun 11, 3772 https://doi.org/10.1038/s41467-020-17541-6
Subramanian, S., Huq, S., Yatsunenko, T., et al. (2014) Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature 510, 417-421 https://doi.org/10.1038/nature13421
Vatanen, T., Kostic A.D., d'Hennezel E., et al. (2016) Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans. Cell 165, 842-853 https://doi.org/10.1016/j.cell.2016.04.007
tse <- SprockettTHData()
#> 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