microbiomeDASim

DOI: 10.18129/B9.bioc.microbiomeDASim    

Microbiome Differential Abundance Simulation

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

PDF	R Script	microbiomeDASim
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Microbiome, Software, Visualization
Version	1.6.0
In Bioconductor since	BioC 3.10 (R-3.6) (2 years)
License	MIT + file LICENSE
Depends	R (>= 3.6.0)
Imports	graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply, stats, phyloseq, metagenomeSeq, Biobase
LinkingTo
Suggests	testthat (>= 2.1.0), knitr, devtools
SystemRequirements
Enhances
URL	https://github.com/williazo/microbiomeDASim
BugReports	https://github.com/williazo/microbiomeDASim/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	microbiomeDASim_1.6.0.tar.gz
Windows Binary	microbiomeDASim_1.6.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	microbiomeDASim_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/microbiomeDASim
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/microbiomeDASim
Package Short Url	https://bioconductor.org/packages/microbiomeDASim/
Package Downloads Report	Download Stats