miaSim

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

Microbiome Data Simulation

Bioconductor version: Development (3.18)

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 "4.3") 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")

miaSim	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Details

biocViews	ATACSeq, Coverage, DNASeq, Microbiome, Network, Sequencing, Software
Version	1.7.2
In Bioconductor since	BioC 3.14 (R-4.1) (2 years)
License	Artistic-2.0 \| file LICENSE
Depends	TreeSummarizedExperiment
Imports	SummarizedExperiment, deSolve, stats, poweRlaw, MatrixGenerics, S4Vectors
Linking To
Suggests	ape, cluster, foreach, doParallel, dplyr, GGally, ggplot2, igraph, network, reshape2, sna, vegan, rmarkdown, knitr, BiocStyle, testthat, mia, miaViz, colourvalues, philentropy
System Requirements
Enhances
URL	https://github.com/microbiome/miaSim
Bug Reports	https://github.com/microbiome/miaSim/issues

Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	miaSim_1.7.2.tar.gz
Windows Binary	miaSim_1.7.2.zip
macOS Binary (x86_64)	miaSim_1.7.2.tgz
macOS Binary (arm64)	miaSim_1.7.2.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