Microbiome Differential Abundance Simulation

This package is developed to simulate microbiome data for longitudinal differential abundance analyses. Microbiome data have a variety of features that make typical simulation methods inappropriate. For an in-depth description of the types of problems this simulation package is designed to solve, plus basics of the functionality please refer to the F1000 manuscript f1000research.20660.2.

Installation

To install the microbiomeDASim package the latest release version is available from Bioconductor

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("microbiomeDASim")

Alternatively to use the latest development version from Bioconductor use the following commands

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("microbiomeDASim", version="devel")

Examples

An interactive examples for how to simulate data from a multivariate normal distribution and fit a trend line using metagenomeSeq::fitTimeSeries are available in the inst/scripts directory.

This notebook can be run interactively using Google Collab by clicking the “Open in Colab” marker at the top of the notebook.