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ArcInstituteArcInstituteOfficial·1 Agent Skills Included

SRAgent

Query SRA genomics data, metadata, and linked publications

Queries the NCBI Sequence Read Archive and GEO to convert accessions, extract sequencing metadata, and identify single-cell technologies. Finds and downloads publications linked to genomics datasets from PubMed, preprint servers, and open-access sources. Eliminates manual database searches and spreadsheet tracking by batch-processing accessions into consolidated metadata reports.
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npx skills add ArcInstitute/SRAgent --all -g -y

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ArcInstituteArcInstitute

sragent

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

Official
Advanced

Frequently Asked Questions

FAQPage Schema
How to install SRAgent?▼

Run `npx skills add ArcInstitute/SRAgent --all -g -y` in your terminal to install all skills in this suite globally.

How to convert GEO accessions to SRA accessions?▼

Ask your agent to convert the accession, and it runs SRAgent's Entrez workflow to map GSE series to SRP studies, SRX experiments, and SRR runs automatically.

Can SRAgent identify single-cell sequencing technology?▼

Yes. It extracts metadata from SRA records, study descriptions, and publications to determine library prep methods such as 10X Genomics chemistry, Smart-seq, or Drop-seq.

How to download papers linked to SRA datasets?▼

Provide an accession or a CSV of accessions, and SRAgent finds linked PubMed IDs and DOIs, then downloads PDFs from preprint servers, CORE, Europe PMC, and Unpaywall.

Does SRAgent require coding experience?▼

No. Once installed, your agent runs the SRAgent command-line workflows from plain-English requests, though API keys for a model provider and NCBI are needed.

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