To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

GEOmetadb

A compilation of metadata from NCBI GEO

Bioconductor version: Release (2.14)

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>

Citation (from within R, enter citation("GEOmetadb")):

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GEOmetadb")

 

PDF R Script GEOmetadb
PDF   Reference Manual

Details

biocViews Infrastructure, Software
Version 1.24.0
In Bioconductor since BioC 2.2 (R-2.7)
License Artistic-2.0
Depends GEOquery, RSQLite
Imports
Suggests
System Requirements
URL http://gbnci.abcc.ncifcrf.gov/geo/
Depends On Me
Imports Me
Suggests Me antiProfilesData

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source GEOmetadb_1.24.0.tar.gz
Windows Binary GEOmetadb_1.24.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) GEOmetadb_1.24.0.tgz
Mac OS X 10.9 (Mavericks) GEOmetadb_1.24.0.tgz
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