alterlab-anndata

What problem does it solve?

AnnData provides a robust, scalable data structure for organizing annotated matrices used in single-cell transcriptomics, enabling researchers to store expression data along with rich cell and gene metadata and multi-resolution annotations.

Core Features & Use Cases

• Core components: X, obs, var, layers, obsm, varm, obsp, varp, uns, and raw storage for preserving original data.
• Interoperability: backed-mode support, sparse matrices, and multi-format I/O (h5ad, Zarr) for large datasets and cloud workflows.
• Use cases: build reproducible pipelines in Scanpy/scverse workflows, perform batch analyses, and prototype analysis by loading only metadata when needed.

Quick Start

Create an AnnData object from your matrix and annotate cells and genes before proceeding with downstream analyses.