recipe bioconductor-bgeedb

Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology

Homepage

https://bioconductor.org/packages/3.11/bioc/html/BgeeDB.html

License

GPL-3 + file LICENSE

Recipe

/bioconductor-bgeedb/meta.yaml

Links

biotools: bgeedb, doi: 10.12688/f1000research.9973.1

A package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.

package bioconductor-bgeedb

Versions

2.14.0-0,  2.12.0-0,  2.10.0-1,  2.8.0-0,  2.6.2-0,  2.4.0-0,  2.2.0-0

Depends

• bioconductor-biobase >=2.48.0,<2.49.0

• bioconductor-graph >=1.66.0,<1.67.0

• bioconductor-topgo >=2.40.0,<2.41.0

• r-base >=4.0,<4.1.0a0

• r-data.table

• r-digest

• r-dplyr

• r-rcurl

• r-rsqlite

• r-tidyr

Required By

• bioconductor-ritan

• bioconductor-psygenet2r

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-bgeedb

and update with:

conda update bioconductor-bgeedb

or use the docker container:

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

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

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-bgeedb/README.html)