miaSim

Microbiome Data Simulation

Bioconductor version: 3.23 · Package version: 1.18.0

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.

Installation

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

BiocManager::install("miaSim")

Details

Maintainer	Yagmur Simsek <yagmur.simsek.98@gmail.com>
Author	Yagmur Simsek [cre, aut], Karoline Faust [aut], Yu Gao [aut], Emma Gheysen [aut], Daniel Rios Garza [aut], Tuomas Borman [aut] (ORCID: <https://orcid.org/0000-0002-8563-8884>), Leo Lahti [aut] (ORCID: <https://orcid.org/0000-0001-5537-637X>), Geraldson Muluh [ctb], Akewak Jeba [ctb] (ORCID: <https://orcid.org/0009-0007-1347-7552>)
License	Artistic-2.0 \| file LICENSE
URL	https://github.com/microbiome/miaSim
Bug Reports	https://github.com/microbiome/miaSim/issues
Downloads rank	256
Source branch	RELEASE_3_23
biocViews	ATACSeq, Coverage, DNASeq, Microbiome, Network, Sequencing, Software

Documentation

miaSim: Microbiome Data Simulation

Download

Source package

Dependencies

Depends: TreeSummarizedExperiment

Imports: SummarizedExperiment, deSolve, stats, poweRlaw, MatrixGenerics, S4Vectors

Suggests: ape, cluster, foreach, doParallel, dplyr, GGally, ggplot2, igraph, network, reshape2, sna, vegan, rmarkdown, knitr, BiocStyle, testthat, mia, miaViz, colourvalues, philentropy