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
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author Khoroshevskyi, Oleksandr
LeRoy, Nathan
Reuter, Vincent P
Sheffield, Nathan C
author_facet Khoroshevskyi, Oleksandr
LeRoy, Nathan
Reuter, Vincent P
Sheffield, Nathan C
author_sort Khoroshevskyi, Oleksandr
collection PubMed
description 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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spelling pubmed-99823562023-03-04 GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA Khoroshevskyi, Oleksandr LeRoy, Nathan Reuter, Vincent P Sheffield, Nathan C Bioinformatics Applications Note 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). Oxford University Press 2023-03-01 /pmc/articles/PMC9982356/ /pubmed/36857584 http://dx.doi.org/10.1093/bioinformatics/btad069 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Khoroshevskyi, Oleksandr
LeRoy, Nathan
Reuter, Vincent P
Sheffield, Nathan C
GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA
title GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA
title_full GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA
title_fullStr GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA
title_full_unstemmed GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA
title_short GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA
title_sort geofetch: a command-line tool for downloading data and standardized metadata from geo and sra
topic Applications Note
url 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
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