GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA

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 G...

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Detalles Bibliográficos
Autores principales: Khoroshevskyi, Oleksandr, LeRoy, Nathan, Reuter, Vincent P, Sheffield, Nathan C
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9982356/
https://www.ncbi.nlm.nih.gov/pubmed/36857584
http://dx.doi.org/10.1093/bioinformatics/btad069
Descripción
Sumario: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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