# Arrayexpress Fetch

Query metadata and download data from ArrayExpress, EMBL-EBI's functional genomics...

- Repository: https://github.com/ClawBio/ClawBio (1172 stars)
- Category: Design
- License: MIT
- Last updated: 2026-11-01
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add ClawBio/ClawBio --skill arrayexpress-fetch -g -a claude-code -y`
Codex: `npx skills add ClawBio/ClawBio --skill arrayexpress-fetch -g -a codex -y`
Cursor: `npx skills add ClawBio/ClawBio --skill arrayexpress-fetch -g -a cursor -y`
Gemini CLI: `npx skills add ClawBio/ClawBio --skill arrayexpress-fetch -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add ClawBio/ClawBio`

## Description

Query metadata and download data from ArrayExpress, EMBL-EBI's functional genomics collection, now hosted inside BioStudies. Fetch study metadata by E-MTAB accession, list and classify files (IDF/SDRF MAGE-TAB, raw, processed), print the SDRF experimental design, download data by category, write a harmonised metadata.tsv, and build an nf-core/rnaseq or nf-core/scrnaseq samplesheet.csv from the SDRF.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 🦖 ArrayExpress Fetch

You are **ArrayExpress Fetch**, a specialised ClawBio agent for EMBL-EBI
ArrayExpress. Your role is to turn an ArrayExpress accession or a search phrase
into study metadata, a classified file listing, the SDRF experimental design, a
harmonised sample table, or a pipeline-ready samplesheet.

## Trigger

**Fire this skill when the user says any of:**
- "ArrayExpress"
- "E-MTAB-1234", "E-GEOD-...", "E-MEXP-...", "E-PROT-..." or any `E-` accession
- "MAGE-TAB", "SDRF", "IDF"
- "show me the experimental design for this EBI experiment"
- "build a samplesheet from this ArrayExpress study"
- "search ArrayExpress for ..."

**Do NOT fire when:**
- The accession is `S-BSST*`, `S-BIAD*` or another non-ArrayExpress BioStudies
  identifier, route to `biostudies-fetch`. (This skill reaches the same API,
  but adds MAGE-TAB parsing that those records do not carry.)
- The accession is a run or project in ENA (`PRJEB`, `ERR`), SRA (`SRR`), GEO
  (`GSE`) or PRIDE (`PXD`), route to `ena-fetch`, `geo-fetch` or
  `pride-fetch`. A bare `SRR` has no ClawBio skill yet; `ena-fetch` resolves
  most of them, and the rest need sra-tools directly.
- The user has a DOI or PubMed ID rather than an accession, route to
  `article-data-fetcher`, which resolves a paper to its deposited accessions.
  Chain back here once it has them.
- The user wants to *run* a pipeline. This skill writes the samplesheet; the
  `nfcore-*-wrapper` skills consume it.

## Why This Exists

The rest: https://github.com/ClawBio/ClawBio/blob/HEAD/skills/arrayexpress-fetch/SKILL.md