API (original) (raw)

Contents

• Combining
• Reading
• Writing
• Experimental API
• Errors and warnings
• Settings
• Custom Types/Classes for Readable/Writeable Elements

API#

The central class:

Combining#

Combining AnnData objects. See also the section on concatenation.

Reading#

Reading anndata’s native formats .h5ad and zarr.

Reading individual portions (obs, varm etc.) of the AnnData object.

Reading file formats that cannot represent all aspects of AnnData objects.

Tip

You might have more success by assembling the AnnData object yourself from the individual parts.

Writing#

Writing a complete AnnData object to disk in anndata’s native formats .h5ad and zarr. (These functions are also exported as io.write_h5ad() and io.write_zarr().)

Writing individual portions (obs, varm etc.) of the AnnData object.

Writing formats that cannot represent all aspects of AnnData objects.

Experimental API#

Warning

APIs in the experimental module are currently in development and subject to change at any time.

Two classes for working with batched access to collections of many AnnData objects or .h5ad files. In particular, for pytorch-based models.

Out of core concatenation

Low level methods for reading and writing elements of an AnnData object to a store:

Utilities for customizing the IO process:

Types used by the former:

Errors and warnings#

Settings#

Custom Types/Classes for Readable/Writeable Elements#