AnnData — Annotated Data (h5ad format)
Overview
AnnData (Annotated Data) is a data format and Python object for single-cell genomics, developed by the Theislab at Helmholtz Munich (Fabian Theis group) and now co-maintained with the Broad Institute. The .h5ad file format (HDF5-based) is the serialised form of AnnData objects and has become a common exchange format for single-cell RNA-seq, ATAC-seq, spatial transcriptomics, and multi-omics data in the Python ecosystem. It stores a cell-by-gene count matrix together with cell metadata, gene metadata, and dimensionality reduction embeddings in a single file.
Connections
- Annotations use: Cell Ontology (cell types), UBERON (anatomy)
- Upstream source: SAM-BAM-CRAM (count matrices from alignment and quantification)