GEOmetadb: A compilation of metadata from NCBI GEO

Share:

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
Date of publication
None
Maintainer
Jack Zhu <zhujack@mail.nih.gov>
License
Artistic-2.0
Version
1.34.0
URLs

View on Bioconductor

Man pages

columnDescriptions
Get column descriptions for the GEOmetadb database
geoConvert
Cross-reference between GEO data types
GEOmetadb-package
Query NCBI GEO metadata from a local SQLite database
getBiocPlatformMap
Get mappings between GPL and Bioconductor microarry...
getSQLiteFile
Download and unzip the most recent GEOmetadb SQLite file

Files in this package

GEOmetadb/.travis.yml
GEOmetadb/DESCRIPTION
GEOmetadb/NAMESPACE
GEOmetadb/R
GEOmetadb/R/columnDescriptions.R
GEOmetadb/R/geoConvert.R
GEOmetadb/R/getBiocPlatformMap.R
GEOmetadb/R/getSQLiteFile.R
GEOmetadb/README.md
GEOmetadb/build
GEOmetadb/build/vignette.rds
GEOmetadb/inst
GEOmetadb/inst/CITATION
GEOmetadb/inst/doc
GEOmetadb/inst/doc/GEOmetadb.R
GEOmetadb/inst/doc/GEOmetadb.Rmd
GEOmetadb/inst/doc/GEOmetadb.html
GEOmetadb/inst/scripts
GEOmetadb/inst/scripts/makeGSErss.R
GEOmetadb/inst/scripts/runTests.R
GEOmetadb/inst/unitTests
GEOmetadb/inst/unitTests/runitDbTests.R
GEOmetadb/man
GEOmetadb/man/GEOmetadb-package.Rd
GEOmetadb/man/columnDescriptions.Rd
GEOmetadb/man/geoConvert.Rd
GEOmetadb/man/getBiocPlatformMap.Rd
GEOmetadb/man/getSQLiteFile.Rd
GEOmetadb/vignettes
GEOmetadb/vignettes/GEOmetadb.Rmd
GEOmetadb/vignettes/GEOmetadb_diagram.pdf
GEOmetadb/vignettes/GEOmetadb_diagram.png