Tooluniverse Expression Data Retrieval

This pulls gene expression and omics datasets from ArrayExpress and BioStudies, with fallback to GEO and other repositories when needed. You give it a gene, condition, or disease, and it returns experiment metadata, sample annotations, file listings, and quality scores based on replication and completeness. The workflow includes gene symbol disambiguation and a three-tier quality assessment system that flags single-replicate studies or sparse metadata. Useful when you need to find RNA-seq or microarray data for specific tissues or conditions before committing to a download. The skill prioritizes experiments with three or more biological replicates and complete raw plus processed data, which saves time filtering through low-quality submissions.

skills.sh installs: 407
GitHub stars: 1.8K
last updated: Aug 21, 2026

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Install

$ npx -y skills add mims-harvard/tooluniverse --skill tooluniverse-expression-data-retrieval --agent claude-code

Installs into .claude/skills of the current project.

Files

Gene Expression & Omics Data Retrieval

Retrieve gene expression experiments and multi-omics datasets with disambiguation and quality assessment.

IMPORTANT: Always use English terms in tool calls. Respond in the user's language.

LOOK UP DON'T GUESS: Never assume which datasets exist or their accessions. Always search to confirm.

Domain Reasoning

Before retrieving, determine: organism, tissue, experimental design (case-control/time-series/dose-response). These affect which database to search and how to interpret results. RNA-seq provides wider dynamic range; microarray has extensive legacy data. Prioritize experiments with >=3 biological replicates, complete annotations, and both raw+processed data.

Workflow

Phase 0: Clarify (if ambiguous) → Phase 1: Disambiguate → Phase 2: Search & Retrieve → Phase 3: Report

Phase 0: Clarification (When Needed)

Ask ONLY if: gene name ambiguous, tissue/condition unclear, organism not specified. Skip for: specific accessions (E-MTAB-, E-GEOD-, S-BSST*), clear disease/tissue+organism, explicit platform requests.