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MDhewei
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geo-download-data

Fetch GEO datasets and parse series_matrix into expression matrices and metadata.

64|12|Updated Apr 7, 2026
Search Tags:#metadata#download#geo#tsv#expression-matrix#series-info
One-click install
npx skills add https://github.com/MDhewei/bioinfor-claw --skill geo-download-data
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: geo-download-data
Source: https://github.com/MDhewei/bioinfor-claw/tree/main/public-datasets-access-and-download/geo-download-data
Command: npx skills add https://github.com/MDhewei/bioinfor-claw --skill geo-download-data

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, pandas, numpy, and includes scripts (resource) components.

What problem does it solve?

Download GEO datasets and metadata from NCBI GEO to enable reproducible data acquisition for downstream analyses.

Core Features & Use Cases

  • Downloads GEO series (GSE) and GEO datasets (GDS) accessions.
  • Extracts expression matrices (expression_matrix.tsv), sample metadata (sample_metadata.tsv), and series information (series_info.json).
  • Optional: download SOFT files for archival purposes and generate a manifest for provenance.

Quick Start

Run the GEO download script by providing an accession and an output directory, for example GSE12345 and data/geo_gse12345

Frequently Asked Questions about geo-download-data

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I download GEO series matrix data and extract an expression matrix?▼

To download GEO data, provide a valid GSE or GDS accession and an output directory. The script fetches the series_matrix from NCBI GEO, decompresses it, and outputs the expression matrix, sample metadata, and series info.

What is the difference between downloading a GSE series and a GDS dataset from NCBI GEO?▼

A GSE series contains individual sample expression data, while a GDS dataset holds curated grouped samples. This download process validates and fetches either accession type from GEO FTP URLs to produce compatible TSV matrices and metadata.

Can I use Python pandas and numpy to parse downloaded GEO expression matrices?▼

Yes, downloaded GEO expression matrices are output as TSV files, which are directly compatible with pandas and numpy. The dependencies are used to parse series_matrix data into structured dataframes for downstream analysis.

Does this GEO download method support retrieving archival SOFT files?▼

Yes, downloading archival SOFT files is supported as an optional feature. Alongside generating TSV expression matrices and JSON series information, the process can retrieve SOFT files to ensure full provenance and reproducibility.

What should I do if my GEO accession format is invalid or the HTTP download fails?▼

The process validates accession formats before attempting retrieval and includes robust error handling with retries for HTTP failures. Ensure your GSE or GDS ID matches expected patterns to avoid format validation errors.

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