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sragent

Convert SRA/GEO accession formats and retrieve associated metadata and publications across CSV batches and BigQuery queries.

177|35|Updated Nov 18, 2024
Search Tags:#bioinformatics#metadata#genomics#single-cell#publications#GEO#SRA
One-click install
npx skills add https://github.com/ArcInstitute/SRAgent --skill sragent
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: sragent
Source: https://github.com/ArcInstitute/SRAgent/tree/main/claude-skill
Command: npx skills add https://github.com/ArcInstitute/SRAgent --skill sragent

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires SRAgent, pandas, and includes references (resource) components.

What problem does it solve?

This Skill automates the complex and time-consuming process of navigating vast genomics databases like SRA/GEO, extracting specific metadata, and finding associated scientific publications. It eliminates manual searching, data conversion, and paper retrieval, allowing researchers to focus on analysis rather than data acquisition.

Core Features & Use Cases

  • Accession Conversion: Seamlessly convert between GEO (GSE), SRA (SRP, SRX, SRR), and ENA (ERX, ERR) accession formats.
  • Metadata Extraction: Automatically pull detailed information like sequencing platform, library prep, organism, and single-cell technology from genomics datasets.
  • Publication Retrieval: Find and download full-text scientific manuscripts linked to SRA accessions from multiple sources.
  • Use Case: A researcher needs to find all human single-cell RNA-seq datasets related to a specific disease, extract their metadata (e.g., 10X Genomics chemistry), and download the associated papers for review. This Skill automates the entire workflow, from initial search to paper delivery.

Quick Start

Convert GEO series GSE121737 to SRX accessions. What 10X Genomics technology was used for experiment ERX11887200? Download papers for SRX4967527.

Frequently Asked Questions about sragent

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

FAQPage Schema
How do I convert between GEO and SRA accession formats?▼

Convert between GEO (GSE), SRA (SRP, SRX, SRR), and ENA (ERX, ERR) accession formats automatically. The Skill handles bidirectional conversion—GSE↔SRP↔SRX↔SRR—allowing you to link datasets across databases without manual lookup.

Can I extract sequencing metadata like platform and library prep from SRA datasets?▼

Extract detailed sequencing metadata including platform, organism, library preparation method, and single-cell technology status directly from SRA/GEO accessions. Outputs structured JSON or CSV suitable for downstream analysis and RAG workflows.

How do I identify single-cell RNA-seq technologies in genomics datasets?▼

Automatically identify scRNA-seq technologies (e.g., 10X Genomics chemistry) from SRA accessions and experiment metadata. The Skill extracts technology-specific information to classify and filter single-cell datasets.

Can I retrieve scientific publications linked to SRA accessions?▼

Download or link related publications associated with SRA/GEO accessions across CSV batches and BigQuery queries. The Skill integrates multiple publication sources to build a complete literature reference set for your datasets.

What environment setup is required to use SRA and GEO metadata tools?▼

Configure OpenAI or Anthropic API keys, NCBI Entrez access, CORE API credentials, and optionally BigQuery for large-scale queries. The Skill depends on SRAgent and pandas for data processing and accession conversion.

Can I batch process multiple accessions and export results to CSV?▼

Process multiple SRA/GEO accessions in batch mode and export results as JSON or CSV files. Structured outputs integrate directly with downstream analysis workflows and research databases.

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