miaSim

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see miaSim.

Microbiome Data Simulation

Bioconductor version: 3.21

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] ORCID iD ORCID: 0000-0002-8563-8884 , Leo Lahti [aut] ORCID iD ORCID: 0000-0001-5537-637X

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

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ATACSeq, Coverage, DNASeq, Microbiome, Network, Sequencing, Software

Version 1.14.0

In Bioconductor since BioC 3.14 (R-4.1) (4 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

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_1.14.0.tar.gz

Windows Binary (x86_64) miaSim_1.14.0.zip

macOS Binary (x86_64) miaSim_1.14.0.tgz

macOS Binary (arm64) miaSim_1.14.0.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/

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