ArticleBioinformatics (Oxford, England)2023
GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Using semantic search to find publicly available gene-expression datasets.Bioinformatics (Oxford, England) · 2026Article
- GEfetch2R: fetching single-cell/bulk RNA-seq data from public repositories to R and benchmarking the subsequent format conversion tools.GigaScience · 2026Article
- EHItk: a toolkit for accessing Earth Hologenome Initiative data resources.Bioinformatics advances · 2026Article
- Atacformer: A transformer-based foundation model for analysis and interpretation of ATAC-seq data.bioRxiv : the preprint server for biology · 2025Article
- MTD: A cloud-based omics database and interactive platform forSynthetic and systems biotechnology · 2025Article
- How far are we from the era of big data in transcriptomics? Lessons from the bacterial data in GEO.Briefings in bioinformatics · 2025Review
- Methods for evaluating unsupervised vector representations of genomic regions.NAR genomics and bioinformatics · 2024Article
- PDL1 targeting by miR-138-5p amplifies anti-tumor immunity and Jurkat cells survival in non-small cell lung cancer.Scientific reports · 2024Article
- PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata.bioRxiv : the preprint server for biology · 2024Article
- OMD Curation Toolkit: a workflow for in-house curation of public omics datasets.BMC bioinformatics · 2024Article
- Joint Representation Learning for Retrieval and Annotation of Genomic Interval Sets.Bioengineering (Basel, Switzerland) · 2024Article
- PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata.GigaScience · 2024Article
- Challenges to sharing sample metadata in computational genomics.Frontiers in genetics · 2023Article
- Opportunities and challenges in sharing and reusing genomic interval data.Frontiers in genetics · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
motivationThe 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.
resultsTo 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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.