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To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("GEOmetadb")
In most cases, you don't need to download the package archive at all.
GEOmetadb
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A compilation of metadata from NCBI GEO
Bioconductor version: Release (3.1)
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:
## try http if https is not available
source("https://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")
| HTML | R Script | GEOmetadb |
| Reference Manual |
Details
| biocViews | Infrastructure, Software |
| Version | 1.28.0 |
| In Bioconductor since | BioC 2.2 (R-2.7) (7.5 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 | |
| Suggests Me | antiProfilesData |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | GEOmetadb_1.28.0.tar.gz |
| Windows Binary | GEOmetadb_1.28.0.zip |
| Mac OS X 10.6 (Snow Leopard) | GEOmetadb_1.28.0.tgz |
| Mac OS X 10.9 (Mavericks) | GEOmetadb_1.28.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/GEOmetadb/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/GEOmetadb/ |
| Package Downloads Report | Download Stats |
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