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Cellxgene census atlas query starter

Skill ma-compbio-lab/SkillFoundry/skills/transcriptomics/cellxgene-census-atlas-query-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install
npx -y skills add ma-compbio-lab/SkillFoundry --skill cellxgene-census-atlas-query-starter

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.1 KB, 275 tokens by cl100k_base, as published. Nobody here has run it

CELLxGENE Census Atlas Query Starter

Use this skill to search the public CELLxGENE Census dataset catalog by keyword and summarize the largest matching atlas datasets.

What it does

  • Opens the public CELLxGENE Census SOMA catalog.
  • Loads the canonical dataset metadata table.
  • Filters dataset titles and collection names by a keyword such as lung, PBMC, or Tabula.
  • Reports top matches, unique collections, and aggregate cell counts.

When to use it

  • You need a reproducible atlas-discovery entry point for multi-sample single-cell workflows.
  • You want to shortlist large public Census datasets before deeper matrix queries.

Example

slurm/envs/census/bin/python skills/transcriptomics/cellxgene-census-atlas-query-starter/scripts/run_cellxgene_census_atlas_query.py \
  --keyword "Tabula Sapiens" \
  --limit 5 \
  --out scratch/census/tabula_sapiens_query.json

Verification

  • Skill-local tests: python3 -m unittest discover -s skills/transcriptomics/cellxgene-census-atlas-query-starter/tests -p 'test_*.py'
  • Repository smoke: python3 -m unittest tests.smoke.test_phase26_frontier_completion_skills -v

Keep looking

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