miaSim

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

Microbiome Data Simulation

Bioconductor version: Development (3.19)

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 "4.4") 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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ATACSeq, Coverage, DNASeq, Microbiome, Network, Sequencing, Software
Version	1.9.0
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

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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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/miaSim
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/miaSim
Package Short Url	https://bioconductor.org/packages/miaSim/
Package Downloads Report	Download Stats