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miaSim

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")):

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")
miaSim HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

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
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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