GEOmetadb-package: Query NCBI GEO metadata from a local SQLite database

Description Details Author(s) References Examples


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.


Package: GEOmetadb
Type: Package
Version: 1.1.5
Date: 2008-09-09
License: Artistic-2.0


Jack Zhu and Sean Davis

Maintainer: Jack Zhu <[email protected]>



if(file.exists('GEOmetadb.sqlite')) {
  a <- columnDescriptions()[1:5,]
  b <- geoConvert('GPL97','GSM')
} else {
  print("use getSQLiteFile() to get a copy of the GEOmetadb SQLite file
and then rerun the example")

Example output

Loading required package: GEOquery
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,, cbind, colMeans, colSums, colnames,,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax,,
    pmin,, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: RSQLite
[1] "use getSQLiteFile() to get a copy of the GEOmetadb SQLite file\nand then rerun the example"

GEOmetadb documentation built on May 2, 2018, 3:52 a.m.