anndata
Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
- Version
- 1.4
- License
- BSD-3-Clause license
- Compatibility
- Requires Python 3.12+ and anndata; uv for installation. Optional dask/lazy extras for lazy I/O; openpyxl for Excel, loompy for legacy Loom, and provider-specific fsspec adapters for remote stores. Network required for installation and remote data only.
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/anndata/SKILL.md
- skills/anndata/SKILL_CN.md
- skills/anndata/references/best_practices.md
- skills/anndata/references/concatenation.md
- skills/anndata/references/data_structure.md
- skills/anndata/references/io_operations.md
- skills/anndata/references/manipulation.md
Every link opens the file at its source, pinned to the revision this page describes.