alterlab-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 ### Does NOT Trigger | Scenario | Use Instead | |----------|-------------| | QC, normalization, HVG, clustering, UMAP, or marker genes | `alterlab-scanpy` | | RNA velocity from spliced/unspliced layers | `alterlab-scvelo` | | Deep generative models / batch integration (scVI, scANVI) | `alterlab-scvi-tools` | | Querying the public CELLxGENE Census for reference cells | `alterlab-cellxgene` | | Chunked n-dimensional arrays outside the AnnData model | `alterlab-zarr` | ## Installation ```bash uv pip install anndata # 0.13.x as of 2026-09; needs Python >= 3.12 # Lazy/backed reads (ad.experimental...