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GEOfetch: a Command-line Tool for Downloading Data and Standardized Metadata from GEO and SRA

Overview
Journal Bioinformatics
Publisher Oxford University Press
Specialty Biology
Date 2023 Mar 1
PMID 36857584
Authors
Oleksandr Khoroshevskyi
Nathan Leroy
Vincent P Reuter
Nathan C Sheffield
Affiliations
Soon will be listed here.
Abstract

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).

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