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CELLxGENE Census Querier

Query versioned public single-cell transcriptomics data from CZ CELLxGENE Census without downloading whole datasets

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
5 files

What it does

Once installed, the agent can search and pull slices of the CZ CELLxGENE Census, a large public collection of standardized single-cell and spatial gene expression data. It can count cells by cell type, tissue, disease or assay, fetch expression data into AnnData format for analysis with Scanpy, and prepare data for machine learning, while pinning a specific Census release so results stay reproducible. It is intended for public reference data, not your own local datasets.

Great for

  • Bioinformaticians who need population-scale cell metadata or expression across many public datasets
  • Researchers comparing their findings against a reference atlas of human or other organism single-cell data
  • Students learning how public single-cell repositories are queried programmatically

Skip it if

  • Analysing your own local single-cell files: the skill itself points to scanpy, anndata or scvi-tools for that
  • Clinical or diagnostic decisions: this is research data access with no validation for medical use
  • Very large queries run without checking memory: the skill warns that cell count alone does not estimate memory needs

Try asking

  • “Count how many primary B cells in the Census come from blood tissue, pinned to the 2025-11-08 release”
  • “Pull expression data for CD4 and CD8A in T cells from COVID-19 donors into an AnnData object”
  • “Check which human datasets in the Census measured a given gene before running an analysis”
  • “Set up a PyTorch data loader over Census cells using TileDB-SOMA-ML”
Step-by-step guide: how to use CELLxGENE Census QuerierInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 5 original files, the MIT licence and an attribution note.

    cellxgene-census.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip cellxgene-census.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip cellxgene-census.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Always include is_primary_data == True in queries to avoid counting the same cell more than once, and pin census_version for reproducible results
  • Check gene symbols carefully using feature_id, since symbols are not guaranteed unique in the current schema
  • Estimate the query size with n_obs and n_vars before loading a large expression matrix into memory

What's inside

  • references/api_access.md
  • references/census_schema.md
  • references/common_patterns.md
  • references/core_workflow_patterns.md
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.