cellxgene-census
Queries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.
- Version
- 1.5
- License
- MIT
- Compatibility
- Requires Linux or macOS, Python 3.10+ and network access to public HTTPS manifests and S3. Tested with Python 3.12, cellxgene-census 1.18.0 and TileDB-SOMA 2.3.0. Spatial export needs the spatial extra; ML needs tiledbsoma-ml and PyTorch. No Census credentials required.
Pinned to revision 68105dd992f1, so it is the text this page describes rather than whatever the author pushed since.
Pre-approved tools experimental
Experimental field. Support varies between clients, so this list is what the author declared, not what your client will enforce.
- Read
- Write
- Edit
- Bash
Files
- skills/cellxgene-census/SKILL.md
- skills/cellxgene-census/SKILL_CN.md
- skills/cellxgene-census/references/api_access.md
- skills/cellxgene-census/references/census_schema.md
- skills/cellxgene-census/references/common_patterns.md
- skills/cellxgene-census/references/core_workflow_patterns.md
Every link opens the file at its source, pinned to the revision this page describes.