GEOmetadb

A compilation of metadata from NCBI GEO

Bioconductor version: 2.8

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 .

Author: Jack Zhu and Sean Davis

Maintainer: Jack Zhu <zhujack at mail.nih.gov>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("GEOmetadb")

To cite this package in a publication, start R and enter:

    citation("GEOmetadb")

Documentation

PDF R Script GEOmetadb
PDF GEOmetadb_diagram.pdf
PDF   Reference Manual

Details

biocViews Infrastructure
Depends GEOquery, RSQLite
Imports
Suggests
System Requirements
License Artistic-2.0
URL http://gbnci.abcc.ncifcrf.gov/geo/
Depends On Me
Imports Me
Suggests Me
Version 1.12.0
Since Bioconductor 2.2 (R-2.7)

Package Downloads

Package Source GEOmetadb_1.12.0.tar.gz
Windows Binary GEOmetadb_1.12.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary GEOmetadb_1.12.0.tgz
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