SilvermanAGutData: SilvermanAGutData
In microbiome/miaTime: Microbiome Time Series Analysis
SilvermanAGutData R Documentation
SilvermanAGutData
Description
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 row 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
Usage
data(SilvermanAGutData)
Format
The data set in
TreeSummarizedExperiment
format.
Value
Loads the data set in R.
Author(s)
Sudarshan A. Shetty and Felix G.M. Ernst
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
microbiome/miaTime documentation built on Nov. 4, 2024, 10:23 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| SilvermanAGutData | R Documentation |
SilvermanAGutData
Description
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 row 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
Usage
data(SilvermanAGutData)
Format
The data set in
TreeSummarizedExperiment
format.
Value
Loads the data set in R.
Author(s)
Sudarshan A. Shetty and Felix G.M. Ernst
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
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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