GEOmetadb
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see GEOmetadb.
A compilation of metadata from NCBI GEO
Bioconductor version: 3.13
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>
citation("GEOmetadb")):
Installation
To install this package, start R (version "4.1") 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")| GEOmetadb | HTML | R Script |
| Reference Manual |
Details
| biocViews | Infrastructure, Software |
| Version | 1.54.0 |
| In Bioconductor since | BioC 2.2 (R-2.7) (16 years) |
| License | Artistic-2.0 |
| Depends | GEOquery, RSQLite |
| Imports | |
| System Requirements | |
| URL | http://gbnci.abcc.ncifcrf.gov/geo/ |
See More
| Suggests | knitr, rmarkdown, dplyr, tm, wordcloud |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | Onassis |
| Suggests Me | antiProfilesData |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GEOmetadb_1.54.0.tar.gz |
| Windows Binary | GEOmetadb_1.54.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | GEOmetadb_1.54.0.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 |
| Old Source Packages for BioC 3.13 | Source Archive |