- recipe bioconductor-miasim
Microbiome Data Simulation
Artistic-2.0 | file LICENSE
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.
- package bioconductor-miasim¶
- depends bioconductor-matrixgenerics:
- depends bioconductor-s4vectors:
- depends bioconductor-summarizedexperiment:
- depends bioconductor-treesummarizedexperiment:
- depends r-base:
- depends r-desolve:
- depends r-powerlaw:
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-miasim and update with:: mamba update bioconductor-miasim
To create a new environment, run:
mamba create --name myenvname bioconductor-miasim
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-miasim:<tag> (see `bioconductor-miasim/tags`_ for valid values for ``<tag>``)