anndata - Annotated Data Matrices for Single-Cell Analysis
Python package for handling annotated data matrices in single-cell genomics with support for h5ad, zarr, and other formats
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 datasets
- transform data
- add metadata
- transpose data
- copy data
- rename observations
- rename variables
- convert strings to categoricals
- access data components
Inputs
- h5ad files
- CSV files
- Loom files
- 10X H5 files
- MTX files
- Excel files
- Zarr directories
- observation metadata
- variable metadata
- data matrices
Outputs
- AnnData objects
- h5ad files
- Zarr files
- CSV files
- filtered data subsets
- concatenated datasets
- transformed data
Requirements
- Python environment
- numpy
- pandas