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miaSim

Microbiome Data Simulation

Bioconductor version: Release (3.17)

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")

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")
caseStudy1-SIS HTML R Script
caseStudy2-NutrientThreshold HTML R Script
caseStudy3-EnvironmentalComplexity HTML R Script
miaSim HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews ATACSeq, Coverage, DNASeq, Microbiome, Network, Sequencing, Software
Version 1.6.0
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, 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
See More
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_1.6.0.tar.gz
Windows Binary miaSim_1.6.0.zip (64-bit only)
macOS Binary (x86_64) miaSim_1.6.0.tgz
macOS Binary (arm64) miaSim_1.6.0.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