recipe bioconductor-biggr

Constraint based modeling in R using metabolic reconstruction databases

Homepage:

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

License:

file LICENSE

Recipe:

/bioconductor-biggr/meta.yaml

This package provides an interface to simulate metabolic reconstruction from the BiGG database(http://bigg.ucsd.edu/) and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs.

package bioconductor-biggr

(downloads) docker_bioconductor-biggr

versions:

1.34.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-1,  1.26.0-0

depends bioconductor-hyperdraw:

>=1.50.0,<1.51.0

depends bioconductor-hypergraph:

>=1.70.0,<1.71.0

depends bioconductor-rsbml:

>=2.56.0,<2.57.0

depends r-base:

>=4.2,<4.3.0a0

depends r-lim:

depends r-limsolve:

depends r-stringr:

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-biggr

and update with::

   mamba update bioconductor-biggr

To create a new environment, run:

mamba create --name myenvname bioconductor-biggr

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-biggr:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-biggr/README.html)