recipe bioconductor-biomart

Interface to BioMart databases (i.e. Ensembl)

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-biomart/meta.yaml

Links:

biotools: biomaRt, doi: 10.1038/nprot.2009.97

In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (<http://www.biomart.org>). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are maintain by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.

package bioconductor-biomart

versions:

2.62.0-0,  2.58.0-0,  2.56.1-0,  2.54.0-0,  2.50.0-0,  2.48.0-0,  2.46.3-0,  2.46.0-0,  2.44.0-0, 

2.62.0-0,  2.58.0-0,  2.56.1-0,  2.54.0-0,  2.50.0-0,  2.48.0-0,  2.46.3-0,  2.46.0-0,  2.44.0-0,  2.42.0-0,  2.40.3-0,  2.38.0-0,  2.36.1-0,  2.34.2-0,  2.34.0-0,  2.32.1-0,  2.30.0-0,  2.28.0-0,  2.27.0-0,  2.26.1-0,  2.26.0-0

depends bioconductor-annotationdbi:

>=1.68.0,<1.69.0

depends bioconductor-biocfilecache:

>=2.14.0,<2.15.0

depends r-base:

>=4.4,<4.5.0a0

depends r-curl:

depends r-digest:

depends r-httr2:

depends r-progress:

depends r-rappdirs:

depends r-stringr:

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-biomart

and update with::

   mamba update bioconductor-biomart

To create a new environment, run:

mamba create --name myenvname bioconductor-biomart

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-biomart:<tag>

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

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