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("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 | ||
NEWS | Text | |
LICENSE | Text |
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 |
See More
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 |