API¶

The central class:

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

An annotated data matrix.

Combining¶

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.

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