GEOmetadb: A compilation of metadata from NCBI GEO

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 .

AuthorJack Zhu and Sean Davis
Date of publicationNone
MaintainerJack Zhu <zhujack@mail.nih.gov>
LicenseArtistic-2.0
Version1.34.0
http://gbnci.abcc.ncifcrf.gov/geo/

View on Bioconductor

Files

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

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