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# API
```{eval-rst}
.. module:: anndata
```
The central class:
```{eval-rst}
.. autosummary::
:toctree: generated/
AnnData
```
(combining-api)=
## Combining
Combining {class}`AnnData` objects.
See also the section on concatenation.
```{eval-rst}
.. autosummary::
:toctree: generated/
concat
```
(reading-api)=
## Reading
Reading anndata’s native formats `.h5ad` and `zarr`.
```{eval-rst}
.. autosummary::
:toctree: generated/
io.read_h5ad
io.read_zarr
```
Reading individual portions ({attr}`~AnnData.obs`, {attr}`~AnnData.varm` etc.) of the {class}`AnnData` object.
```{eval-rst}
.. autosummary::
:toctree: generated/
io.read_elem
io.sparse_dataset
```
Reading file formats that cannot represent all aspects of {class}`AnnData` objects.
```{tip}
You might have more success by assembling the {class}`AnnData` object yourself from the individual parts.
```
```{eval-rst}
.. autosummary::
:toctree: generated/
io.read_csv
io.read_excel
io.read_hdf
io.read_loom
io.read_mtx
io.read_text
io.read_umi_tools
```
(writing-api)=
## Writing
Writing a complete {class}`AnnData` object to disk in anndata’s native formats `.h5ad` and `zarr`.
(These functions are also exported as {func}`io.write_h5ad` and {func}`io.write_zarr`.)
```{eval-rst}
.. autosummary::
:toctree: generated/
AnnData.write_h5ad
AnnData.write_zarr
..
.. autosummary::
:toctree: generated/
io.write_h5ad
io.write_zarr
.. toctree::
:hidden:
generated/anndata.io.write_h5ad
generated/anndata.io.write_zarr
```
Writing individual portions ({attr}`~AnnData.obs`, {attr}`~AnnData.varm` etc.) of the {class}`AnnData` object.
```{eval-rst}
.. autosummary::
:toctree: generated/
io.write_elem
```
Writing formats that cannot represent all aspects of {class}`AnnData` objects.
```{eval-rst}
.. autosummary::
:toctree: generated/
AnnData.write_csvs
AnnData.write_loom
```
(experimental-api)=
## 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 {class}`AnnData` objects or `.h5ad` files.
In particular, for pytorch-based models.
```{eval-rst}
.. autosummary::
:toctree: generated/
experimental.AnnCollection
experimental.AnnLoader
```
Out of core concatenation
```{eval-rst}
.. autosummary::
:toctree: generated/
experimental.concat_on_disk
```
Low level methods for reading and writing elements of an {class}`AnnData` object to a store:
```{eval-rst}
.. autosummary::
:toctree: generated/
experimental.read_elem_lazy
experimental.read_lazy
```
Utilities for customizing the IO process:
```{eval-rst}
.. autosummary::
:toctree: generated/
experimental.read_dispatched
experimental.write_dispatched
```
Types used by the former:
```{eval-rst}
.. autosummary::
:toctree: generated/
experimental.IOSpec
experimental.Read
experimental.Write
experimental.ReadCallback
experimental.WriteCallback
experimental.StorageType
experimental.backed._lazy_arrays.MaskedArray
experimental.backed._lazy_arrays.CategoricalArray
experimental.backed._xarray.Dataset2D
```
(extensions-api)=
## Extensions
```{eval-rst}
.. autosummary::
:toctree: generated/
register_anndata_namespace
```
Types used by the former:
```{eval-rst}
.. autosummary::
:toctree: generated/
types.ExtensionNamespace
```
(errors-api)=
## Errors and warnings
```{eval-rst}
.. autosummary::
:toctree: generated/
ImplicitModificationWarning
```
(settings-api)=
## Settings
```{eval-rst}
.. autosummary::
:toctree: generated/
settings
settings.override
```
(types-api)=
## Custom Types/Classes for Readable/Writeable Elements
```{eval-rst}
.. autosummary::
:toctree: generated/
abc.CSRDataset
abc.CSCDataset
typing.Index
typing.AxisStorable
typing.RWAble
```
|
