DOI: 10.18129/B9.bioc.miaSim  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see miaSim.

Microbiome Data Simulation

Bioconductor version: 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>

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HTML R Script caseStudy1-SIS
HTML R Script caseStudy2-NutrientThreshold
HTML R Script caseStudy3-EnvironmentalComplexity
HTML R Script miaSim
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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
Suggests ape, cluster, dplyr, GGally, ggplot2, igraph, network, reshape2, sna, vegan, rmarkdown, knitr, BiocStyle, testthat, mia, miaViz, colourvalues, philentropy
URL https://github.com/microbiome/miaSim
BugReports https://github.com/microbiome/miaSim/issues
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Source Package miaSim_1.6.0.tar.gz
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