recipe bioconductor-gosemsim

GO-terms Semantic Similarity Measures

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-gosemsim/meta.yaml

Links:

biotools: gosemsim

The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively.

package bioconductor-gosemsim

versions:

2.32.0-0,  2.28.0-1,  2.28.0-0,  2.26.0-0,  2.24.0-1,  2.24.0-0,  2.20.0-2,  2.20.0-1,  2.20.0-0, 

2.32.0-0,  2.28.0-1,  2.28.0-0,  2.26.0-0,  2.24.0-1,  2.24.0-0,  2.20.0-2,  2.20.0-1,  2.20.0-0,  2.18.0-0,  2.16.1-0,  2.16.0-0,  2.14.0-0,  2.12.0-0,  2.10.0-1,  2.8.0-0,  2.6.2-0,  2.4.0-0,  2.2.0-1,  2.2.0-0,  1.30.3-0,  1.29.0-0,  1.28.2-0

depends bioconductor-annotationdbi:

>=1.68.0,<1.69.0

depends bioconductor-annotationdbi:

>=1.68.0,<1.69.0a0

depends bioconductor-go.db:

>=3.20.0,<3.21.0

depends bioconductor-go.db:

>=3.20.0,<3.21.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libcxx:

>=18

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.4,<4.5.0a0

depends r-dbi:

depends r-digest:

depends r-r.utils:

depends r-rcpp:

depends r-rlang:

depends r-yulab.utils:

>=0.1.6

requirements:

additional platforms:

linux-aarch64

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-gosemsim

and update with::

   mamba update bioconductor-gosemsim

To create a new environment, run:

mamba create --name myenvname bioconductor-gosemsim

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-gosemsim:<tag>

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

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Link to this page

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