oral_mouthwash_data

This dataset contains a matrix and a data frame: genus-level microbiome profiles and
corresponding sample metadata from an oral microbiome perturbation study.
28 participants' oral microbiomes were measured before, 15 minutes after, and 2 hours
after perturbation with either a water control, antiseptic mouthwash, alchohol-free mouthwash,
or soda. The dataset is used in examples and vignettes throughout the package.

datasets

Provides scalable generalized linear and mixed effects models tailored for sequence count data analysis (e.g., analysis of 16S or RNA-seq data). Uses Dirichlet-multinomial sampling to quantify uncertainty in relative abundance or relative expression conditioned on observed count data.
Implements scale models as a generalization of normalizations which account for uncertainty in scale (e.g., total abundances) as described in Nixon et al. (2025) <doi:10.1186/s13059-025-03609-3> and McGovern et al. (2025) <doi:10.1101/2025.08.05.668734>.

Justin Silverman

ALDEx3

Linear Models for Sequence Count Data

Greg Gloor

Kyle McGovern

oral_mouthwash_data function

A named list of one matrix and a dataframe:<dl>
<dt><code>counts</code></dt>
<dd>A matrix with read counts with 116 rows and 81 columns)</dd><dt><code>metadata</code></dt>
<dd>A data frame with 81 rows and 38 columns containing sample-level covariates.</dd>
</dl>

Format

Oral microbiome perturbation dataset (list) — oral_mouthwash_data

A named list of one matrix and a dataframe:<dl>
<dt><code>counts</code></dt>
<dd>A matrix with read counts with 116 rows and 81 columns)</dd>

<dt><code>metadata</code></dt>
<dd>A data frame with 81 rows and 38 columns containing sample-level covariates.</dd>


</dl>

oral_mouthwash_data: Oral microbiome perturbation dataset (list)

Description

Usage

Arguments

Format

Details