recipe bioconductor-biomartgogenesets

Gene Ontology Gene Sets from BioMart

Homepage:

https://bioconductor.org/packages/3.18/data/annotation/html/BioMartGOGeneSets.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-biomartgogenesets/meta.yaml

It contains pre-compiled Gene Ontology gene sets for all organisms available on the Ensembl database. It also includes GO gene sets for organisms on Ensembl Plants, Ensembl Metazoa, Ensembl Fungi and Ensembl Protists. The data was collected with the biomaRt package.

package bioconductor-biomartgogenesets

(downloads) docker_bioconductor-biomartgogenesets

versions:

0.99.11-0

depends bioconductor-data-packages:

>=20231203

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends curl:

depends r-base:

>=4.3,<4.4.0a0

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-biomartgogenesets

and update with::

   mamba update bioconductor-biomartgogenesets

To create a new environment, run:

mamba create --name myenvname bioconductor-biomartgogenesets

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-biomartgogenesets:<tag>

(see `bioconductor-biomartgogenesets/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-biomartgogenesets/README.html)