miaSim

Microbiome Data Simulation

Bioconductor version: Release (3.20)

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")

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	1.12.0
In Bioconductor since	BioC 3.14 (R-4.1) (3 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
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.

Source Package	miaSim_1.12.0.tar.gz
Windows Binary (x86_64)	miaSim_1.12.0.zip
macOS Binary (x86_64)	miaSim_1.12.0.tgz
macOS Binary (arm64)	miaSim_1.12.0.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