networkvi.model.NETWORKVI
=========================

.. currentmodule:: networkvi.model

.. add toctree option to make autodoc generate the pages

.. autoclass:: NETWORKVI



Attributes table
~~~~~~~~~~~~~~~~~~

.. autosummary::

    ~networkvi.model.NETWORKVI.adata
    ~networkvi.model.NETWORKVI.adata_manager
    ~networkvi.model.NETWORKVI.device
    ~networkvi.model.NETWORKVI.history
    ~networkvi.model.NETWORKVI.is_trained
    ~networkvi.model.NETWORKVI.summary_string
    ~networkvi.model.NETWORKVI.test_indices
    ~networkvi.model.NETWORKVI.train_indices
    ~networkvi.model.NETWORKVI.validation_indices





Methods table
~~~~~~~~~~~~~

.. autosummary::

    ~networkvi.model.NETWORKVI.calculate_covariate_attention
    ~networkvi.model.NETWORKVI.convert_legacy_save
    ~networkvi.model.NETWORKVI.deregister_manager
    ~networkvi.model.NETWORKVI.differential_accessibility
    ~networkvi.model.NETWORKVI.differential_expression
    ~networkvi.model.NETWORKVI.get_accessibility_estimates
    ~networkvi.model.NETWORKVI.get_anndata_manager
    ~networkvi.model.NETWORKVI.get_elbo
    ~networkvi.model.NETWORKVI.get_from_registry
    ~networkvi.model.NETWORKVI.get_go_gene_importances
    ~networkvi.model.NETWORKVI.get_latent_representation
    ~networkvi.model.NETWORKVI.get_library_size_factors
    ~networkvi.model.NETWORKVI.get_marginal_ll
    ~networkvi.model.NETWORKVI.get_normalized_expression
    ~networkvi.model.NETWORKVI.get_perturbation_go_gene_importances
    ~networkvi.model.NETWORKVI.get_protein_foreground_probability
    ~networkvi.model.NETWORKVI.get_reconstruction_error
    ~networkvi.model.NETWORKVI.get_region_factors
    ~networkvi.model.NETWORKVI.load
    ~networkvi.model.NETWORKVI.load_query_data
    ~networkvi.model.NETWORKVI.load_registry
    ~networkvi.model.NETWORKVI.prepare_query_anndata
    ~networkvi.model.NETWORKVI.register_manager
    ~networkvi.model.NETWORKVI.save
    ~networkvi.model.NETWORKVI.setup_anndata
    ~networkvi.model.NETWORKVI.to_device
    ~networkvi.model.NETWORKVI.train
    ~networkvi.model.NETWORKVI.view_anndata_setup
    ~networkvi.model.NETWORKVI.view_setup_args





Attributes
~~~~~~~~~~~



.. autoattribute:: NETWORKVI.adata

.. autoattribute:: NETWORKVI.adata_manager

.. autoattribute:: NETWORKVI.device

.. autoattribute:: NETWORKVI.history

.. autoattribute:: NETWORKVI.is_trained

.. autoattribute:: NETWORKVI.summary_string

.. autoattribute:: NETWORKVI.test_indices

.. autoattribute:: NETWORKVI.train_indices

.. autoattribute:: NETWORKVI.validation_indices






Methods
~~~~~~~



.. automethod:: NETWORKVI.calculate_covariate_attention

.. automethod:: NETWORKVI.convert_legacy_save

.. automethod:: NETWORKVI.deregister_manager

.. automethod:: NETWORKVI.differential_accessibility

.. automethod:: NETWORKVI.differential_expression

.. automethod:: NETWORKVI.get_accessibility_estimates

.. automethod:: NETWORKVI.get_anndata_manager

.. automethod:: NETWORKVI.get_elbo

.. automethod:: NETWORKVI.get_from_registry

.. automethod:: NETWORKVI.get_go_gene_importances

.. automethod:: NETWORKVI.get_latent_representation

.. automethod:: NETWORKVI.get_library_size_factors

.. automethod:: NETWORKVI.get_marginal_ll

.. automethod:: NETWORKVI.get_normalized_expression

.. automethod:: NETWORKVI.get_perturbation_go_gene_importances

.. automethod:: NETWORKVI.get_protein_foreground_probability

.. automethod:: NETWORKVI.get_reconstruction_error

.. automethod:: NETWORKVI.get_region_factors

.. automethod:: NETWORKVI.load

.. automethod:: NETWORKVI.load_query_data

.. automethod:: NETWORKVI.load_registry

.. automethod:: NETWORKVI.prepare_query_anndata

.. automethod:: NETWORKVI.register_manager

.. automethod:: NETWORKVI.save

.. automethod:: NETWORKVI.setup_anndata

.. automethod:: NETWORKVI.to_device

.. automethod:: NETWORKVI.train

.. automethod:: NETWORKVI.view_anndata_setup

.. automethod:: NETWORKVI.view_setup_args