miaSim
Microbiome Data Simulation
Bioconductor version: 3.24 · Package version: 1.19.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("miaSim")Details
| Maintainer | Yagmur Simsek <yagmur.simsek.98@gmail.com> |
| Author | Yagmur Simsek [cre, aut], Karoline Faust [aut], Yu Gao [aut], Emma Gheysen [aut], Daniel Rios Garza [aut], Tuomas Borman [aut] (ORCID: <https://orcid.org/0000-0002-8563-8884>), Leo Lahti [aut] (ORCID: <https://orcid.org/0000-0001-5537-637X>), Geraldson Muluh [ctb], Akewak Jeba [ctb] (ORCID: <https://orcid.org/0009-0007-1347-7552>) |
| License | Artistic-2.0 | file LICENSE |
| URL | https://github.com/microbiome/miaSim |
| Bug Reports | https://github.com/microbiome/miaSim/issues |
| Downloads rank | 399 |
| Source branch | devel |
| biocViews | ATACSeq, Coverage, DNASeq, Microbiome, Network, Sequencing, Software |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | miaSim_1.19.0.tar.gz |
| Windows binary (x86_64) | miaSim_1.19.0.zip |
| macOS binary (arm64) | miaSim_1.19.0.tgz |
| macOS binary (x86_64) | miaSim_1.19.0.tgz |
Dependencies
Depends: TreeSummarizedExperiment
Imports: SummarizedExperiment, deSolve, stats, poweRlaw, MatrixGenerics, S4Vectors
Suggests: ape, cluster, foreach, doParallel, dplyr, GGally, ggplot2, igraph, network, reshape2, sna, vegan, rmarkdown, knitr, BiocStyle, testthat, mia, miaViz, colourvalues, philentropy