GEOmetadb

DOI: 10.18129/B9.bioc.GEOmetadb    

A compilation of metadata from NCBI GEO

Bioconductor version: Release (3.6)

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:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GEOmetadb")

Documentation

HTML	R Script	GEOmetadb
PDF		Reference Manual

Details

biocViews	Infrastructure, Software
Version	1.40.0
In Bioconductor since	BioC 2.2 (R-2.7) (10 years)
License	Artistic-2.0
Depends	GEOquery, RSQLite
Imports
LinkingTo
Suggests	knitr, rmarkdown, dplyr, tm, wordcloud
SystemRequirements
Enhances
URL	http://gbnci.abcc.ncifcrf.gov/geo/
Depends On Me
Imports Me	Onassis
Suggests Me	antiProfilesData
Build Report

Package Archives

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

Source Package	GEOmetadb_1.40.0.tar.gz
Windows Binary	GEOmetadb_1.38.1.zip
Mac OS X 10.11 (El Capitan)	GEOmetadb_1.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GEOmetadb
Package Short Url	http://bioconductor.org/packages/GEOmetadb/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive