Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.
Department of Biomedical Engineering, School of Medicine, University of Virginia, Charlottesville, VA 22904, USA.
Bioinformatics. 2023 Mar 1;39(3). doi: 10.1093/bioinformatics/btad069.
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).
基因表达综合数据库已成为用于二次分析的重要生物数据资源。然而,目前没有简单的、编程式的方法可以以标准化注释格式从基因表达综合数据库(GEO)下载数据和元数据。
针对这一问题,我们提供了 GEOfetch,这是一个命令行工具,可以从 GEO 和 SRA 下载和组织数据和元数据。GEOfetch 将下载的元数据格式化为可移植封装项目,为公共数据的重新分析提供了通用格式。
GEOfetch 可在 Bioconda 和 Python 包索引(PyPI)上使用。