Retrieve GEO datasets and metadata using GEOparse and NCBI E-utilities.
npx skills add https://github.com/OwnLabAI/ownlab --skill geo-database-ownlabai
Please help me install this Agent Skill. Skill: geo-database Source: https://github.com/OwnLabAI/ownlab/tree/main/mart/skills/scientific-skills/geo-database Command: npx skills add https://github.com/OwnLabAI/ownlab --skill geo-database-ownlabai
GEO datasets are scattered across multiple GEO resources (Series, Samples, Platforms, and supplementary files), making discovery, extraction, and consistent downstream analyses labor-intensive and error-prone.
Find a GEO study of interest and run a script to fetch its GSE, GPL, and GSM data for downstream processing.
High-intent search queries and answers about installing and using this skill.
To retrieve GEO datasets, you can use this skill to identify and fetch GSE, GSM, and GPL records along with their metadata. It leverages GEOparse and NCBI E-utilities to automate data collection for reproducible downstream transcriptomics pipelines.
Mapping GEO platform probes to genes requires retrieving platform annotations, which this skill provides. It fetches GPL data to map probes to genes, enabling consistent cross-study data integration across different experiments and platforms.
Filtering GEO datasets by organism, data type, platform, and publication date is supported. This allows you to curate specific study sets necessary for conducting accurate meta-analyses across multiple transcriptomics experiments.
Automating GEO data collection is best achieved by programmatically accessing metadata via GEOparse and NCBI E-utilities. This skill applies these tools to provide robust data retrieval, ensuring your GEO data collection remains fully reproducible.
Yes, GEOparse works alongside NCBI E-utilities and GEO FTP access to fetch GSE and GSM records. This combination provides robust data retrieval and platform annotation mapping for downstream transcriptomics analyses.
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