miaSim

DOI: 10.18129/B9.bioc.miaSim  

Microbiome Data Simulation

Bioconductor version: Release (3.17)

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 (Tree)SummarizedExperiment objects.

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

Maintainer: Yagmur Simsek <yagmur.simsek.98 at gmail.com>

Installation

To install this package, start R (version "4.3") 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	caseStudy1-SIS
HTML	R Script	caseStudy2-NutrientThreshold
HTML	R Script	caseStudy3-EnvironmentalComplexity
HTML	R Script	miaSim
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ATACSeq, Coverage, DNASeq, Microbiome, Network, Sequencing, Software
Version	1.6.0
In Bioconductor since	BioC 3.14 (R-4.1) (2 years)
License	Artistic-2.0 | file LICENSE
Depends	TreeSummarizedExperiment
Imports	SummarizedExperiment, deSolve, stats, poweRlaw, MatrixGenerics, S4Vectors
LinkingTo
Suggests	ape, cluster, dplyr, GGally, ggplot2, igraph, network, reshape2, sna, vegan, rmarkdown, knitr, BiocStyle, testthat, mia, miaViz, colourvalues, philentropy
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_1.6.0.tar.gz
Windows Binary	miaSim_1.6.0.zip (64-bit only)
macOS Binary (x86_64)	miaSim_1.6.0.tgz
macOS Binary (arm64)	miaSim_1.6.0.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
Old Source Packages for BioC 3.17	Source Archive