recipe bioconductor-interminer

R Interface with InterMine-Powered Databases

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/InterMineR.html

License:

LGPL

Recipe:

/bioconductor-interminer/meta.yaml

Databases based on the InterMine platform such as FlyMine, modMine (modENCODE), RatMine, YeastMine, HumanMine and TargetMine are integrated databases of genomic, expression and protein data for various organisms. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge. This R package provides interfaces with these databases through webservices. It makes most from the correspondence of the data frame object in R and the table object in databases, while hiding the details of data exchange through XML or JSON.

package bioconductor-interminer

versions:

1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.1-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.1-0, 

1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.1-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.1-0,  1.4.1-0,  1.2.1-0,  1.0.0-0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends r-base:

>=4.3,<4.4.0a0

depends r-httr:

depends r-igraph:

depends r-rcurl:

depends r-rjsonio:

depends r-sqldf:

depends r-xml:

depends r-xml2:

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-interminer

and update with::

   mamba update bioconductor-interminer

To create a new environment, run:

mamba create --name myenvname bioconductor-interminer

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-interminer:<tag>

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

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Link to this page

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-interminer/README.html)