SprockettTHData: Obtain the Sprockett Tsimane Horticulturalists data
In microbiome/microbiomeDataSets: Experiment Hub based microbiome datasets
View source: R/SprockettTHData.R
SprockettTHData R Documentation
Obtain the Sprockett Tsimane Horticulturalists data
Description
Obtain the microbiome data from Sprockett et al. (2020).
Usage
SprockettTHData()
Details
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.
Value
a TreeSummarizedExperiment
Author(s)
Sudarshan A. Shetty and Felix G.M. Ernst
References
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
Examples
tse <- SprockettTHData()
microbiome/microbiomeDataSets documentation built on Sept. 25, 2024, 11:42 p.m.
R Package Documentation
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View source: R/SprockettTHData.R
| SprockettTHData | R Documentation |
Obtain the Sprockett Tsimane Horticulturalists data
Description
Obtain the microbiome data from Sprockett et al. (2020).
Usage
SprockettTHData()
Details
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.
Value
a TreeSummarizedExperiment
Author(s)
Sudarshan A. Shetty and Felix G.M. Ernst
References
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
Examples
tse <- SprockettTHData()
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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