GEOmetadb

DOI: 10.18129/B9.bioc.GEOmetadb  

A compilation of metadata from NCBI GEO

Bioconductor version: Release (3.16)

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 (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GEOmetadb")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("GEOmetadb")

 

HTML	R Script	GEOmetadb
PDF		Reference Manual

Details

biocViews	Infrastructure, Software
Version	1.60.0
In Bioconductor since	BioC 2.2 (R-2.7) (15 years)
License	Artistic-2.0
Depends	GEOquery, RSQLite
Imports
LinkingTo
Suggests	knitr, rmarkdown, dplyr, tm, wordcloud
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	MetaIntegrator
Suggests Me	antiProfilesData
Links To Me
Build Report

Package Archives

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

Source Package	GEOmetadb_1.60.0.tar.gz
Windows Binary	GEOmetadb_1.60.0.zip
macOS Binary (x86_64)	GEOmetadb_1.60.0.tgz
macOS Binary (arm64)	GEOmetadb_1.60.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GEOmetadb
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GEOmetadb
Bioc Package Browser	https://code.bioconductor.org/browse/GEOmetadb/
Package Short Url	https://bioconductor.org/packages/GEOmetadb/
Package Downloads Report	Download Stats