anndata

AnnData Overview AnnData is a Python package for handling annotated data matrices, storing experimental measurements (X) alongside observation metadata (obs), variable metadata (var), and multi-dimensional annotations (obsm, varm, obsp, varp, uns). Originally designed for single-cell genomics through Scanpy, it now serves as a general-purpose framework for any annotated data requiring efficient storage, manipulation, and analysis. When to Use This Skill Use this skill when: Creating, reading, or writing AnnData objects Working with h5ad, zarr, or other genomics data formats Performing single-cell RNA-seq analysis Managing large datasets with sparse matrices or backed mode Concatenating multiple datasets or experimental batches Subsetting, filtering, or transforming annotated data Integrating with scanpy, scvi-tools, or other scverse ecosystem tools Installation Show more