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>
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 | ||
| 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) (2.5 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 |
See More
| Suggests | ape, cluster, 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_1.6.0.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 |
| Old Source Packages for BioC 3.17 | Source Archive |