miaSim

DOI: 10.18129/B9.bioc.miaSim    

This is the development version of miaSim; for the stable release version, see miaSim.

Microbiome Data Simulation

Bioconductor version: Development (3.15)

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>

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.0
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
License Artistic-2.0 | file LICENSE
Depends SummarizedExperiment
Imports deSolve, stats, poweRlaw
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_1.1.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) miaSim_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/miaSim
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/miaSim
Package Short Url https://bioconductor.org/packages/miaSim/
Package Downloads Report Download Stats

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