recipe bioconductor-geometadb

A compilation of metadata from NCBI GEO

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/GEOmetadb.html

License:

Artistic-2.0

Recipe:

/bioconductor-geometadb/meta.yaml

Links:

biotools: 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 .

package bioconductor-geometadb

(downloads) docker_bioconductor-geometadb

versions:
1.64.0-0,  1.62.0-0,  1.60.0-0,  1.56.0-0,  1.54.0-0,  1.52.0-1,  1.52.0-0,  1.50.0-0,  1.48.0-0, 

1.64.0-0,  1.62.0-0,  1.60.0-0,  1.56.0-0,  1.54.0-0,  1.52.0-1,  1.52.0-0,  1.50.0-0,  1.48.0-0,  1.46.0-1,  1.44.0-0,  1.42.0-0,  1.40.0-0

depends bioconductor-geoquery:

>=2.70.0,<2.71.0

depends r-base:

>=4.3,<4.4.0a0

depends r-rsqlite:

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-geometadb

and update with::

   mamba update bioconductor-geometadb

To create a new environment, run:

mamba create --name myenvname bioconductor-geometadb

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-geometadb:<tag>

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

Download stats

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)