The central class:

AnnData([X, obs, var, uns, obsm, varm, …])

An annotated data matrix.


Reading anndata’s native file format .h5ad.

read_h5ad(filename[, backed, chunk_size])

Read .h5ad-formatted hdf5 file.

Reading other file formats.

read_csv(filename[, delimiter, …])

Read .csv file.

read_excel(filename, sheet[, dtype])

Read .xlsx (Excel) file.

read_hdf(filename, key)

Read .h5 (hdf5) file.

read_loom(filename[, sparse, cleanup, …])

Read .loom-formatted hdf5 file.

read_mtx(filename[, dtype])

Read .mtx file.

read_text(filename[, delimiter, …])

Read .txt, .tab, .data (text) file.

read_umi_tools(filename[, dtype])

Read a gzipped condensed count matrix from umi_tools.


Read from a hierarchical Zarr array store.


Writing to anndata’s native file format .h5ad.

AnnData.write([filename, compression, …])

Write .h5ad-formatted hdf5 file.

Writing to other formats.

AnnData.write_csvs(dirname[, skip_data, sep])

Write annotation to .csv files.

AnnData.write_loom(filename[, write_obsm_varm])

Write .loom-formatted hdf5 file.

AnnData.write_zarr(store[, chunks])

Write a hierarchical Zarr array store.


Independent of AnnData, the submodule anndata.h5py provides a thin wrapper of h5py that is able to handle sparse matrices in addition to the standard functionality.


Wraps h5py to handle sparse matrices.