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microbiomeDASim

Microbiome Differential Abundance Simulation

Bioconductor version: Release (3.17)

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 "4.3") 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

Details

biocViews Microbiome, Software, Visualization
Version 1.14.0
In Bioconductor since BioC 3.10 (R-3.6) (4 years)
License MIT + file LICENSE
Depends R (>= 3.6.0)
Imports graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply, stats, phyloseq, metagenomeSeq, Biobase
Linking To
Suggests testthat (>= 2.1.0), knitr, devtools
System Requirements
Enhances
URL https://github.com/williazo/microbiomeDASim
Bug Reports https://github.com/williazo/microbiomeDASim/issues
See More
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_1.14.0.tar.gz
Windows Binary microbiomeDASim_1.14.0.zip
macOS Binary (x86_64) microbiomeDASim_1.14.0.tgz
macOS Binary (arm64) microbiomeDASim_1.14.0.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/
Package Downloads Report Download Stats