recipe bioconductor-simona

Semantic Similarity in Bio-Ontologies

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/simona.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-simona/meta.yaml

This package implements infrastructures for ontology analysis by offering efficient data structures, fast ontology traversal methods, and elegant visualizations. It provides a robust toolbox supporting over 70 methods for semantic similarity analysis.

package bioconductor-simona

versions:

1.4.0-0,  1.0.2-0

depends bioconductor-complexheatmap:

>=2.22.0,<2.23.0

depends bioconductor-complexheatmap:

>=2.22.0,<2.23.0a0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends perl:

>=5.32.1,<5.33.0a0 *_perl5

depends perl:

>=5.6.0

depends r-base:

>=4.4,<4.5.0a0

depends r-circlize:

depends r-getoptlong:

depends r-globaloptions:

depends r-igraph:

depends r-matrixstats:

depends r-polychrome:

depends r-rcpp:

depends r-shiny:

depends r-xml2:

>=1.3.3

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-simona

and update with::

   mamba update bioconductor-simona

To create a new environment, run:

mamba create --name myenvname bioconductor-simona

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-simona:<tag>

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

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