Individual skill
cellxgene-census
Programmatically query the CZ CELLxGENE Census (61M+ cells) when you need cross-tissue, disease, or cell-type expression data for population-scale queries and reference atlas comparisons.
scientific-skills/Evidence Insight/cellxgene-census/SKILL.md
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- bioinformatics Repository topic
- computational-biology Repository topic
- data-analysis Repository topic
- ai Repository topic
- biology Repository topic
- cancer-genomics Repository topic
- data-visualization Repository topic
- differential-expression Repository topic
- genomics Repository topic
- medical Repository topic
- data Derived category
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SKILL.mdcore · 6,500 bytesSKILL.mdcore · 6,500 bytesSKILL.mdcore · 6,500 bytesSKILL.mdcore · 6,500 bytesSKILL.mdcore · 6,500 bytescellxgene-census_audit_result_v1.jsonasset · 12,164 bytesreferences/census_schema.mddoc · 6,001 bytesreferences/common_patterns.mddoc · 10,398 bytes
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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)
## When to Use
- **Cross-tissue or cross-disease expression comparisons** (e.g., macrophages across lung/liver/brain; COVID-19 vs control).
- **Reference atlas lookups** to contextualize findings from your own single-cell dataset (marker validation, expected expression patterns).
- **Population-scale metadata exploration** (what tissues/cell types/datasets exist; cell counts by cohort attributes).
- **Large-scale expression statistics** where results exceed RAM and require out-of-core iteration.
- **Model training on curated atlas data** (e.g., cell-type classifiers) using the experimental PyTorch integration.
## Key Features
- Programmatic access to **versioned** CZ CELLxGENE Census data (human and mouse).
- Query **cell (obs) metadata** and **gene (var) metadata** with expressive filter syntax.
- Retrieve expression as **AnnData** for small/medium queries via `get_anndata()`.