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Can GEO data be accessed programmatically?

April 26, 2017accessed Data Geo programmatically

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Can GEO data be accessed programmatically?

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Yes. Users can take advantage of NCBI’s Entrez programming utilities to access data stored in Entrez GEO DataSets and Entrez GEO Profiles… more information and examples. Additionally, BioConductor users may be interested in the GEOquery package which parses GEO SOFT files for integration with BioConductor ‘R’ analysis resources, see publication. What is GEO BLAST? The GEO BLAST tool queries Entrez GEO Profiles for molecular abundance profiles of interest based on nucleotide sequence similarity. The GEO BLAST database contains all GenBank sequences represented on microarray Platforms or SAGE libraries in GEO. This interface is helpful in identifying sequence homologs of interest, e.g., related gene family members or for cross-species comparisons.

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Yes. Users can take advantage of NCBI’s Entrez programming utilities to access data stored in Entrez GEO DataSets and Entrez GEO Profiles (more information and examples). Additionally, BioConductor users may be interested in the GEOquery package which parses GEO SOFT files for integration with BioConductor ‘R’ analysis resources, see publication.