GEOmetadb-package: Query NCBI GEO metadata from a local SQLite database

In GEOmetadb: A compilation of metadata from NCBI GEO

Description

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.

Details

Package:	GEOmetadb
Type:	Package
Version:	1.1.5
Date:	2008-09-09
License:	Artistic-2.0

Author(s)

Jack Zhu and Sean Davis

Maintainer: Jack Zhu <[e-mail]>

Examples

## Use the demo GEOmetadb database:
if( !file.exists("GEOmetadb.sqlite") ) {
    demo_sqlfile <- getSQLiteFile(destdir = getwd(), destfile = "GEOmetadb.sqlite.gz", type = "demo")
} else {
    demo_sqlfile <- "GEOmetadb.sqlite"
}
columnDescriptions(demo_sqlfile)[1:5,]
a <- columnDescriptions(demo_sqlfile)[1:5,]
b <- geoConvert('GPL96', out_type='GSM', sqlite_db_name=demo_sqlfile)

## Download the full GEOmetadb database:
## Not run: geometadbfile <- getSQLiteFile()

GEOmetadb documentation built on Nov. 8, 2020, 7:19 p.m.