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AnnData is the Python object, saved as an .h5ad file, that holds an expression matrix together with its per-cell and per-gene annotations; it is the lingua franca of single-cell analysis.
The anndata documentation describes an annotated data matrix: observations (cells or samples) by variables (genes), with data frames of metadata for each axis, unstructured metadata and layers, stored on disk in HDF5 as .h5ad. Scanpy, CELLxGENE and most single-cell foundation models read and write it, and bulk transcriptome models such as BulkFormer publish their TCGA matrices in the same format. OnCo lists anndata on the open-source map.
Shares Single-cell RNA sequencing (scRNA-seq, 10x Chromium), CZ CELLxGENE / Human Cell Atlas, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Array and table formats: HDF5, Zarr, OME-Zarr, Parquet, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Single-cell RNA sequencing (scRNA-seq, 10x Chromium), CZ CELLxGENE / Human Cell Atlas, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Array and table formats: HDF5, Zarr, OME-Zarr, Parquet, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Single-cell RNA sequencing (scRNA-seq, 10x Chromium), Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Single-cell RNA sequencing (scRNA-seq, 10x Chromium), Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Single-cell RNA sequencing (scRNA-seq, 10x Chromium), Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Single-cell RNA sequencing (scRNA-seq, 10x Chromium), Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.