microbiomeDASim

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see microbiomeDASim.

Microbiome Differential Abundance Simulation

Bioconductor version: 3.20

A toolkit for simulating differential microbiome data designed for longitudinal analyses. Several functional forms may be specified for the mean trend. Observations are drawn from a multivariate normal model. The objective of this package is to be able to simulate data in order to accurately compare different longitudinal methods for differential abundance.

Author: Justin Williams, Hector Corrada Bravo, Jennifer Tom, Joseph Nathaniel Paulson

Maintainer: Justin Williams <williazo at ucla.edu>

Citation (from within R, enter citation("microbiomeDASim")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("microbiomeDASim")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("microbiomeDASim")

microbiomeDASim PDF R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Microbiome, Software, Visualization

Version 1.20.0

In Bioconductor since BioC 3.10 (R-3.6) (5.5 years)

License MIT + file LICENSE

Depends R (>= 3.6.0)

Imports graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply, stats, phyloseq, metagenomeSeq, Biobase

System Requirements

URL https://github.com/williazo/microbiomeDASim

Bug Reports https://github.com/williazo/microbiomeDASim/issues

Suggests testthat (>= 2.1.0), knitr, devtools

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package microbiomeDASim_1.20.0.tar.gz

Windows Binary (x86_64) microbiomeDASim_1.20.0.zip (64-bit only)

macOS Binary (x86_64) microbiomeDASim_1.20.0.tgz

macOS Binary (arm64) microbiomeDASim_1.20.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/microbiomeDASim

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/microbiomeDASim

Bioc Package Browser https://code.bioconductor.org/browse/microbiomeDASim/

Package Short Url https://bioconductor.org/packages/microbiomeDASim/

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