recipe bioconductor-geometadb

A compilation of metadata from NCBI GEO

Homepage:

https://bioconductor.org/packages/3.20/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:
1.72.0-0,  1.68.1-0,  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, 

1.72.0-0,  1.68.1-0,  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:

  • on r-base >=4.5,<4.6.0a0

  • on r-r.utils

  • on r-rsqlite

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-geometadb

to add into an existing workspace instead, run:

pixi add bioconductor-geometadb

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-geometadb

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-geometadb

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-geometadb:<tag>

(see bioconductor-geometadb/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.

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