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Querying the CELLxGENE Census for single-cell data v1.0.0

Use this resource to query versioned public single-cell data from the Census

New

  • 381 downloads
  • 181 likes
  • 194 saves

Free

Install with the CLI

In a terminal, from the folder you want:

npx --yes palatekit@latest install single-cell-census-queries

With no option, the skill goes to ~/.agents/skills/; add --agent claude-code (or codex, cursor…) to target an agent.

First time: connect the CLI with

npx --yes palatekit@latest login

The agent pins the Census version, filters to primary data, estimates query size, then loads only the cells needed. You get reproducible query code and counts to check.

Mostly picked by

Updated November 2, 2026

Card for the “Querying the CELLxGENE Census for single-cell data” skill

Details

Works in
Install guides
Generates with
Your agent's model
Licence
MIT

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What you get

  • SKILL.md: installation, query patterns and filtering best practices
  • references/: API access, Census schema, common query patterns and core workflows

Good fit for

  • You want cells of a given type and tissue across several studies
  • You compare your data with a public atlas

Not for

    Tags

    • single-cell
    • Census
    • transcriptomics

    About

    You say

    “Extract CD3E expression in T cells from human lung, using a pinned Census version.”

    Card for the “Querying the CELLxGENE Census for single-cell data” skill

    Skill published by k-dense-ai under the MIT license, delivered in its original version.

    Show more

    How to use it

    1. Install the skill in your agent's skills folder
    2. Ask your agent to query versioned public single-cell data from the Census
    3. Review and adjust the result

    Content preview

    Files

    • LICENSE1.1 KB
    • NOTICE-PALATEKIT.md0.5 KB
    • references/api_access.md5.9 KB
    • references/census_schema.md9.5 KB
    • references/common_patterns.md15.6 KB
    • references/core_workflow_patterns.md11 KB
    • SKILL.md13.7 KB

    Origin and licence

    Listed unmodified

    Author
    k-dense-ai
    Source
    github.com/k-dense-ai/scientific-agent-skills/tree/5f2bc0341354fd5590aef76a533ada1e1e5b4e62/skills/cellxgene-census
    Licence
    MIT

    Notice

    « cellxgene-census » (k-dense-ai, MIT) livré dans sa version d'origine : fiche en français et en anglais par PalateKit.

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