Package Recipe 'bioconductor-interminer'

recipe bioconductor-interminer

R Interface with InterMine-Powered Databases

Homepage:: https://bioconductor.org/packages/3.18/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:

1.24.0-0, 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,

1.24.0-0, 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:

on bioconductor-biostrings >=2.70.0,<2.71.0
on bioconductor-genomicranges >=1.54.0,<1.55.0
on bioconductor-iranges >=2.36.0,<2.37.0
on bioconductor-s4vectors >=0.40.0,<0.41.0
on bioconductor-summarizedexperiment >=1.32.0,<1.33.0
on r-base >=4.3,<4.4.0a0
on r-httr
on r-igraph
on r-rcurl
on r-rjsonio
on r-sqldf
on r-xml
on r-xml2

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-interminer

to add into an existing workspace instead, run:

pixi add bioconductor-interminer

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-interminer

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-interminer

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-interminer:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an 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-interminer/README.html)