Motivation

The Gene Expression Omnibus has become an important source of biological data for secondary analysis. However, there is no simple, programmatic way to download data and metadata from Gene Expression Omnibus (GEO) in a standardized annotation format.

Results

To address this, we present GEOfetch—a command-line tool that downloads and organizes data and metadata from GEO and SRA. GEOfetch formats the downloaded metadata as a Portable Encapsulated Project, providing universal format for the reanalysis of public data.

Availability and implementation

GEOfetch is available on Bioconda and the Python Package Index (PyPI).

© The Author(s) 2023. Published by Oxford University Press.
2023
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