Package: GEOmetadb 1.74.0
Jack Zhu
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
Authors:
GEOmetadb_1.74.0.tar.gz
GEOmetadb_1.74.0.zip(r-4.7)GEOmetadb_1.74.0.zip(r-4.6)GEOmetadb_1.74.0.zip(r-4.5)
GEOmetadb_1.74.0.tgz(r-4.6-any)GEOmetadb_1.74.0.tgz(r-4.5-any)
GEOmetadb_1.74.0.tar.gz(r-4.7-any)GEOmetadb_1.74.0.tar.gz(r-4.6-any)
GEOmetadb_1.74.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
GEOmetadb/json (API)
| # Install 'GEOmetadb' in R: |
| install.packages('GEOmetadb', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:GEOmetadb-1.75.0(bioc 3.24)GEOmetadb-1.74.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:b213e297ec (on RELEASE_3_23). Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 138 | ||
| linux-devel-x86_64 | WARNING | 166 | ||
| source / vignettes | OK | 222 | ||
| linux-release-x86_64 | WARNING | 193 | ||
| macos-release-arm64 | WARNING | 112 | ||
| macos-oldrel-arm64 | WARNING | 91 | ||
| windows-devel | WARNING | 129 | ||
| windows-release | WARNING | 92 | ||
| windows-oldrel | WARNING | 99 | ||
| wasm-release | OK | 117 |
Exports:columnDescriptionsgeoConvertgetBiocPlatformMapgetSQLiteFile
Dependencies:bitbit64blobcachemclicpp11DBIfastmapgluelifecyclememoisepkgconfigR.methodsS3R.ooR.utilsrlangRSQLitevctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Query NCBI GEO metadata from a local SQLite database | GEOmetadb-package GEOmetadb |
| Get column descriptions for the GEOmetadb database | columnDescriptions |
| Cross-reference between GEO data types | geoConvert |
| Get mappings between GPL and Bioconductor microarry annotation packages | getBiocPlatformMap |
| Download and unzip the most recent GEOmetadb SQLite file | getSQLiteFile |
