minimalgut: Human Gut Minimal Microbiome Profiling Data
In microbiome/miaTime: Microbiome Time Series Analysis
minimalgut R Documentation
Human Gut Minimal Microbiome Profiling Data
Description
This time-series data set contains absolute temporal abundances
for 16 human gut species that were assembled in an in vitro gut system. These
were subjected to a variety of disturbances over a period of 20 days. The
sample data includes measurements for Acetate, Butyrate, Propionate, and
optical density.
Usage
data(minimalgut)
Format
The data set in
TreeSummarizedExperiment
format.
Details
The data is available also on
https://github.com/microsud/syncomR
The data contains 183 samples from 3 in vitro gut system, 61 per bioreactor
collected three times daily.
The current implementation in miaTime provides this as
TreeSummarizedExperiment
object.
Value
Loads the data set in R.
Author(s)
Sudarshan A. Shetty
References
Shetty, S.A., Kostopoulos, I., Geerlings, S.Y. et al. Dynamic metabolic
interactions and trophic roles of human gut microbes identified using a
minimal microbiome exhibiting ecological properties.
ISME, 16, 2144–2159 (2022). https://doi.org/10.1038/s41396-022-01255-2.
microbiome/miaTime documentation built on Nov. 4, 2024, 10:23 p.m.
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| minimalgut | R Documentation |
Human Gut Minimal Microbiome Profiling Data
Description
This time-series data set contains absolute temporal abundances for 16 human gut species that were assembled in an in vitro gut system. These were subjected to a variety of disturbances over a period of 20 days. The sample data includes measurements for Acetate, Butyrate, Propionate, and optical density.
Usage
data(minimalgut)
Format
The data set in
TreeSummarizedExperiment
format.
Details
The data is available also on
https://github.com/microsud/syncomR
The data contains 183 samples from 3 in vitro gut system, 61 per bioreactor
collected three times daily.
The current implementation in miaTime provides this as
TreeSummarizedExperiment
object.
Value
Loads the data set in R.
Author(s)
Sudarshan A. Shetty
References
Shetty, S.A., Kostopoulos, I., Geerlings, S.Y. et al. Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties. ISME, 16, 2144–2159 (2022). https://doi.org/10.1038/s41396-022-01255-2.
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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