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singlecell-portal

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Programmatically query public single-cell study metadata from the Broad Institute Single Cell Portal REST API when you need to search and filter datasets by organism, tissue, disease, or cell type without an API key.

scientific-skills/Data Analysis/singlecell-portal/SKILL.md

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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)

## When to Use

- You need to **discover relevant public single-cell studies** by filtering on organism (e.g., human/mouse) and tissue (e.g., lung/brain).
- You want to **quickly retrieve study-level metadata** (e.g., study name, accession, cell counts) for downstream curation or reporting.
- You are building a script or tool that needs **no authentication** and should work reliably on **Windows** with minimal setup.
- You want to **inspect available filter facets** (what tissues/diseases/cell types exist in the index) before constructing queries.
- You need a lightweight way to **validate that a study exists** and fetch its details by accession.

## Key Features

- Direct REST access to the official Single Cell Portal API (`/single_cell/api/v1/*`)
- No API key required (public endpoints)
- Faceted search for studies (organism, tissue, disease, cell type, etc.)
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