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geo-data

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Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror. Use when finding expression datasets, navigating SuperSeries vs SubSeries, choosing between series-matrix (submitter-normalized) and raw supplementary files, downloading via GEOparse (Python) or GEOquery (R/Bioconductor), linking GEO to SRA for raw reads, or distinguishing GSE/GSM/GPL/GDS record types. Encodes the SuperSeries trap, the series-matrix normalization-trust caveat, GEOmetadb deprecation, ArrayExpress migration to BioStudies, and processed-vs-raw decision matrix.

When to use

• finding expression datasets
• navigating SuperSeries vs SubSeries
• choosing between series-matrix and raw supplementary files
• downloading via GEOparse or GEOquery
• linking GEO to SRA for raw reads
• distinguishing GSE/GSM/GPL/GDS record types
• querying NCBI Gene Expression Omnibus
• querying EMBL-EBI BioStudies/ArrayExpress mirror

When not to use

• creating new GDS records
• using GEOmetadb

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