Tag: GEO

GEOmetadb 1.52.0 – GEO Microarray Search Tool

GEOmetadb 1.52.0

:: DESCRIPTION

GEOmetadb is an attempt to make access to the metadata associated with the NCBI Gene Expression Omnibus (GEO) samples, platforms, and datasets much more feasible for common biologists and bioinformatians/statistians.

::DEVELOPER

Jack Zhu , Sean Davis @NCI

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 GEOmetadb

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Dec 1;24(23):2798-800. doi: 10.1093/bioinformatics/btn520.
GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus.
Zhu Y, Davis S, Stephens R, Meltzer PS, Chen Y.

GEOquery 2.58.0 – Get data from NCBI Gene Expression Omnibus (GEO)

GEOquery 2.58.0

:: DESCRIPTION

GEOquery effectively establishes a bridge between GEO and BioConductor. Easy access to GEO data from BioConductor will likely lead to new analyses of GEO data using novel and rigorous statistical and bioinformatic tools.

::DEVELOPER

Sean Davis @NCI

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 GEOquery

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Jul 15;23(14):1846-7.
GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor.
Davis S, Meltzer PS.

GEO2Enrichr – Browser Extension for Extracting Differentially Expressed Gene Sets from GEO

GEO2Enrichr

:: DESCRIPTION

GEO2Enrichr is web application and two browser extensions (one for Chrome and another for Firefox) designed to facilitate the extraction of signatures from studies posted on the Gene Expression Omnibus (GEO) database.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Chrome / Firefox

:: DOWNLOAD

GEO2Enrichr

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Sep 15;31(18):3060-2. doi: 10.1093/bioinformatics/btv297. Epub 2015 May 13.
GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions.
Gundersen GW, Jones MR, Rouillard AD, Kou Y, Monteiro CD, Feldmann AS, Hu KS, Ma’ayan A.

MARQ – Mine GEO for Experiments with Similar or opposite Gene Expression Signatures

MARQ

:: DESCRIPTION

MARQ (Microarray Rank Query) is an online microarray retrieval tool based on rank statistics. Datasets in MARQ, most of them retrieved from GEO, are processed into signatures, which are lists of genes ranked by their level of differential expression. Each dataset defines one of more of these signatures based on the possible comparisons of its constituent samples.

::DEVELOPER

MARQ team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

Vazquez, M., Nogales-Cadenas, R., Arroyo, J., Botías, P., García, R., Carazo, J. M., Tirado, F., Pascual-Montano, A. Carmona-Saez, P. 2010,
`MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures.’ ,
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W228-32.