Version Compatibility

Reference examples tested with: BioPython 1.83+, Entrez Direct 21.0+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

GEO Data

Query and access Gene Expression Omnibus datasets using Biopython's Entrez module.

"Find expression datasets in GEO" → Search GEO for microarray/RNA-seq datasets by organism, tissue, or condition, then download expression matrices or link to SRA runs.

• Python: Entrez.esearch(db='gds', term=...) (BioPython)
• CLI: esearch -db gds -query "term" (Entrez Direct)