miaSim

DOI: 10.18129/B9.bioc.miaSim  

Microbiome Data Simulation

Bioconductor version: Release (3.16)

Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell's Neutral model is used to determine the abundance matrix. The resulting abundance matrix is applied to SummarizedExperiment or TreeSummarizedExperiment objects.

Author: Karoline Faust [aut], Yu Gao [aut], Emma Gheysen [aut], Daniel Rios Garza [aut], Yagmur Simsek [cre, aut], Leo Lahti [aut]

Maintainer: Yagmur Simsek <yagmur.simsek at hsrw.org>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("miaSim")

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("miaSim")

 

HTML	R Script	miaSim
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ATACSeq, Coverage, DNASeq, Microbiome, Network, Sequencing, Software
Version	1.4.0
In Bioconductor since	BioC 3.14 (R-4.1) (1.5 years)
License	Artistic-2.0 | file LICENSE
Depends	SummarizedExperiment, TreeSummarizedExperiment
Imports	deSolve, stats, poweRlaw, gtools, S4Vectors, MatrixGenerics
LinkingTo
Suggests	rmarkdown, knitr, BiocStyle, testthat
SystemRequirements
Enhances
URL	https://github.com/microbiome/miaSim
BugReports	https://github.com/microbiome/miaSim/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	miaSim_1.4.0.tar.gz
Windows Binary	miaSim_1.4.0.zip
macOS Binary (x86_64)	miaSim_1.4.0.tgz
macOS Binary (arm64)	miaSim_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/miaSim
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/miaSim
Bioc Package Browser	https://code.bioconductor.org/browse/miaSim/
Package Short Url	https://bioconductor.org/packages/miaSim/
Package Downloads Report	Download Stats