Welcome to the new bioconductor.org!


Microbiome Data Simulation

Bioconductor version: Release (3.18)

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>

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


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

miaSim HTML R Script
Reference Manual PDF


biocViews ATACSeq, Coverage, DNASeq, Microbiome, Network, Sequencing, Software
Version 1.8.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License Artistic-2.0 | file LICENSE
Depends TreeSummarizedExperiment
Imports SummarizedExperiment, deSolve, stats, poweRlaw, MatrixGenerics, S4Vectors
System Requirements
URL https://github.com/microbiome/miaSim
Bug Reports https://github.com/microbiome/miaSim/issues
See More
Suggests ape, cluster, foreach, doParallel, dplyr, GGally, ggplot2, igraph, network, reshape2, sna, vegan, rmarkdown, knitr, BiocStyle, testthat, mia, miaViz, colourvalues, philentropy
Linking To
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package miaSim_1.8.0.tar.gz
Windows Binary miaSim_1.8.0.zip
macOS Binary (x86_64) miaSim_1.8.0.tgz
macOS Binary (arm64) miaSim_1.8.0.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