anndata - Annotated data structure for genomics
Python package for annotated data matrices in single-cell genomics
Tags
Updated: 2026-06-30Capabilities
Typical Inputs
Typical Outputs
What this skill does
- create AnnData objects
- read h5ad files
- write h5ad files
- read CSV files
- read loom files
- read 10X h5 files
- write zarr files
- write CSV files
- subset data
- filter data
- concatenate objects
- transpose data
- copy objects
- convert sparse matrices
- access metadata
- backed mode read
- compress data
Inputs
- h5ad files
- CSV files
- loom files
- 10X h5 files
- zarr directories
- numpy arrays
- pandas DataFrames
Outputs
- h5ad files
- zarr directories
- CSV directories
- AnnData objects
- data subsets
- compressed files
Requirements
- Python environment
- uv pip
- scipy for sparse matrices
- scanpy for analysis workflows
- scvi-tools for probabilistic models
- cellxgene-census for population-scale queries