anndata-data-structure
AnnData — Annotated Data Matrices for Single-Cell Genomics
Overview
AnnData provides the standard data structure for single-cell genomics in the scverse ecosystem. It stores an observations-by-variables matrix (X) alongside cell metadata (obs), gene metadata (var), layers, embeddings (obsm/varm), graphs (obsp/varp), and unstructured metadata (uns). Supports sparse matrices, H5AD/Zarr storage, backed mode for large files, and integration with Scanpy, scvi-tools, and Muon.
When to Use
- Constructing annotated matrices from raw count data with cell/gene metadata
- Reading/writing
.h5ador.zarrfiles for single-cell experiments - Subsetting cells by quality metrics, gene sets, or metadata conditions
- Concatenating multiple experimental batches with consistent metadata
- Storing multiple data layers (raw counts, normalized, scaled) in one object
- Working with large datasets exceeding RAM (backed mode, lazy concatenation)
- Preparing data for Scanpy or scvi-tools pipelines
- For single-cell analysis (clustering, DE, visualization), use
scanpyinstead - For probabilistic models, use
scvi-toolsinstead
Prerequisites
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