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Bioconductor - miaSim (development version)

miaSim

This is the development version of miaSim; for the stable release version, see miaSim.

Microbiome Data Simulation

Bioconductor version: Development (3.22)

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: 0000-0002-8563-8884 , Leo Lahti [aut] 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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews ATACSeq, Coverage, DNASeq, Microbiome, Network, Sequencing, Software Version 1.15.0 In Bioconductor since BioC 3.14 (R-4.1) (3.5 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 Enhances 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.

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