recipe bioconductor-sparsedossa

Sparse Data Observations for Simulating Synthetic Abundance

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/sparseDOSSA.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-sparsedossa/meta.yaml

The package is to provide a model based Bayesian method to characterize and simulate microbiome data. sparseDOSSA's model captures the marginal distribution of each microbial feature as a truncated, zero-inflated log-normal distribution, with parameters distributed as a parent log-normal distribution. The model can be effectively fit to reference microbial datasets in order to parameterize their microbes and communities, or to simulate synthetic datasets of similar population structure. Most importantly, it allows users to include both known feature-feature and feature-metadata correlation structures and thus provides a gold standard to enable benchmarking of statistical methods for metagenomic data analysis.

package bioconductor-sparsedossa

versions:

1.24.0-0,  1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1, 

1.24.0-0,  1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.1-0

depends r-base:

>=4.3,<4.4.0a0

depends r-mass:

depends r-mcmcpack:

depends r-optparse:

depends r-tmvtnorm:

>=1.4.10

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

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-sparsedossa

and update with::

   mamba update bioconductor-sparsedossa

To create a new environment, run:

mamba create --name myenvname bioconductor-sparsedossa

with myenvname being 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-sparsedossa:<tag>

(see `bioconductor-sparsedossa/tags`_ for valid values for ``<tag>``)

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Link to this page

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