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

GEOmetadb

A compilation of metadata from NCBI GEO

Bioconductor version: 2.13

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>

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		GEOmetadb_diagram.pdf
PDF		Reference Manual

Details

biocViews	Infrastructure, Software
Version	1.22.0
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_1.22.0.tar.gz
Windows Binary	GEOmetadb_1.22.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	GEOmetadb_1.22.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats