recipe bioconductor-tidysbml

Extract SBML's data into dataframes

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/tidysbml.html

License:

CC BY 4.0

Recipe:

/bioconductor-tidysbml/meta.yaml

Starting from one SBML file, it extracts information from each listOfCompartments, listOfSpecies and listOfReactions element by saving them into data frames. Each table provides one row for each entity (i.e. either compartment, species, reaction or speciesReference) and one set of columns for the attributes, one column for the content of the 'notes' subelement and one set of columns for the content of the 'annotation' subelement.

package bioconductor-tidysbml

versions:

1.0.0-0

depends r-base:

>=4.4,<4.5.0a0

depends r-xml2:

requirements:

additional platforms:

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-tidysbml

and update with::

   mamba update bioconductor-tidysbml

To create a new environment, run:

mamba create --name myenvname bioconductor-tidysbml

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-tidysbml:<tag>

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

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