The central class:

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

An annotated data matrix.


Combining AnnData objects. See also the section on concatenation.

concat(adatas, *[, axis, join, merge, …])

Concatenates AnnData objects along an axis.


Reading anndata’s native file format .h5ad.

read_h5ad(filename[, backed, as_sparse, …])

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_zarr(*_, **__)


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.

Errors and warnings


Raised whenever initializing an object or assigning a property changes the type of a part of a parameter or the value being assigned.