GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA.
other · Level V
Where this comes from
- Record sourced from PubMed, PMID 36857584.
- Also identified by DOI 10.1093/bioinformatics/btad069 and PMC identifier 9982356.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. 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. GEOfetch is available on Bioconda and the Python Package Index (PyPI).
Medical subject headings
- Metadata
- Gene Expression