gut_crohns_data

This dataset contains a matrix and a data frame: genus-level microbiome profiles and
corresponding sample metadata from a Crohn's disease case–control cohort.
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

gut_crohns_data function

A named list of one matrix and a dataframe:<dl>
<dt><code>counts</code></dt>
<dd>A matrix with read counts with 195 rows and 95 columns)</dd><dt><code>metadata</code></dt>
<dd>A data frame with 95 rows and 7 columns containing subject-level covariates.</dd>
</dl>

Format

Gut Crohn's microbiome dataset (list) — gut_crohns_data

A named list of one matrix and a dataframe:<dl>
<dt><code>counts</code></dt>
<dd>A matrix with read counts with 195 rows and 95 columns)</dd>

<dt><code>metadata</code></dt>
<dd>A data frame with 95 rows and 7 columns containing subject-level covariates.</dd>


</dl>

gut_crohns_data: Gut Crohn's microbiome dataset (list)

Description

Usage

Arguments

Format

Details