recipe bioconductor-geometadb

The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and datasets much more feasible. This is accomplished by parsing all the NCBI GEO metadata into a SQLite database that can be stored and queried locally. GEOmetadb is simply a thin wrapper around the SQLite database along with associated documentation. Finally, the SQLite database is updated regularly as new data is added to GEO and can be downloaded at will for the most up-to-date metadata. GEOmetadb paper: http://bioinformatics.oxfordjournals.org/cgi/content/short/24/23/2798 .

Homepage

https://bioconductor.org/packages/3.9/bioc/html/GEOmetadb.html

License

Artistic-2.0

Recipe

/bioconductor-geometadb/meta.yaml

Links

biotools: geometadb

package bioconductor-geometadb

(downloads) docker_bioconductor-geometadb

Versions

1.44.0-0, 1.42.0-0, 1.40.0-0

Depends bioconductor-geoquery

>=2.50.0,<2.51.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-rsqlite

Requirements

Installation

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

conda install bioconductor-geometadb

and update with:

conda update bioconductor-geometadb

or use the docker container:

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

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

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-geometadb/README.html)