alcohol: Datasets
In abichat/zazou: Z-Scores As Ornstein-Uhlenbeck
Description
Usage
Format
Details
Source
Description
alcohol, chlamydiae and age datasets
Usage
1
2
3
4
5
Format
A list containing
Xthe normalized OTU data,
Ythe alcohol intake phenotype,
treethe corresponding phylogenetic tree,
taxonomythe taxonomic lineages of the OTUs.
Details
The alcohol dataset was taken from a study of the dietary
association with the gut microbiome (Wu, 2011). Here we include the
alcohol intake as the primary phenotype. The OTU abundance data consists
of 98 samples with 949 OTUs with prevalence > 10
normalized to account for variable library sizes.
The chlamydia dataset is taken from a 16s rRNA diversity study
narrowed to the Chlamydiae bacteria taxon, originally appearing in PNAS.
The age dataset comes from Brito et al. (2016)
Source
Wu, Gary D., et al. "Linking long-term dietary patterns with gut
microbial enterotypes." Science 334.6052 (2011): 105-108.
Caporaso, J. G., et al. (2011). "Global patterns of 16S rRNA
diversity at a depth of millions of sequences per sample." PNAS,
108, 4516-4522. PMCID: PMC3063599
Brito, Ilana L., et al. "Mobile genes in the human microbiome
are structured from global to individual scales." Nature 535.7612
(2016): 435-439.
abichat/zazou documentation built on Sept. 8, 2021, 6:53 a.m.
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Description Usage Format Details Source
Description
alcohol, chlamydiae and age datasets
Usage
1 2 3 4 5 |
Format
A list containing
Xthe normalized OTU data,
Ythe alcohol intake phenotype,
treethe corresponding phylogenetic tree,
taxonomythe taxonomic lineages of the OTUs.
Details
The alcohol dataset was taken from a study of the dietary
association with the gut microbiome (Wu, 2011). Here we include the
alcohol intake as the primary phenotype. The OTU abundance data consists
of 98 samples with 949 OTUs with prevalence > 10
normalized to account for variable library sizes.
The chlamydia dataset is taken from a 16s rRNA diversity study
narrowed to the Chlamydiae bacteria taxon, originally appearing in PNAS.
The age dataset comes from Brito et al. (2016)
Source
Wu, Gary D., et al. "Linking long-term dietary patterns with gut microbial enterotypes." Science 334.6052 (2011): 105-108.
Caporaso, J. G., et al. (2011). "Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample." PNAS, 108, 4516-4522. PMCID: PMC3063599
Brito, Ilana L., et al. "Mobile genes in the human microbiome are structured from global to individual scales." Nature 535.7612 (2016): 435-439.
R Package Documentation
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