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 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
- relatedTo: Cell Ontology (obs annotations in brain cell atlas AnnData objects are conventionally coded using Cell Ontology cell type terms)
- relatedTo: UBERON (tissue and brain region annotations in brain cell atlas AnnData objects are conventionally coded using UBERON terms)