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Developer

Import scvi-tools as:

import scvi

.. currentmodule:: scvi

Data Registration

.. currentmodule:: scvi

AnnDataFields delineate how scvi-tools refers to fields in AnnData objects. The AnnDataManager provides an interface for operating over a collection of AnnDataFields and an AnnData object.

.. autosummary::
   :toctree: reference/
   :nosignatures:

   data.AnnDataManager
   data.AnnDataManagerValidationCheck
   data.fields.BaseAnnDataField
   data.fields.LayerField
   data.fields.CategoricalObsField
   data.fields.CategoricalVarField
   data.fields.NumericalJointObsField
   data.fields.NumericalJointVarField
   data.fields.CategoricalJointObsField
   data.fields.CategoricalJointVarField
   data.fields.ObsmField
   data.fields.VarmField
   data.fields.ProteinObsmField
   data.fields.StringUnsField
   data.fields.LabelsWithUnlabeledObsField
   data.fields.BaseMuDataWrapperClass
   data.fields.MuDataWrapper
   data.fields.MuDataLayerField
   data.fields.MuDataProteinLayerField
   data.fields.MuDataNumericalObsField
   data.fields.MuDataNumericalVarField
   data.fields.MuDataCategoricalObsField
   data.fields.MuDataCategoricalVarField
   data.fields.MuDataObsmField
   data.fields.MuDataVarmField
   data.fields.MuDataNumericalJointObsField
   data.fields.MuDataNumericalJointVarField
   data.fields.MuDataCategoricalJointObsField
   data.fields.MuDataCategoricalJointVarField
   data.AnnTorchDataset

Data Loaders

.. currentmodule:: scvi

DataLoaders for loading tensors from AnnData objects. DataSplitters for splitting data into train/test/val.

.. autosummary::
   :toctree: reference/
   :nosignatures:

   dataloaders.AnnDataLoader
   dataloaders.AnnTorchDataset
   dataloaders.CollectionAdapter
   dataloaders.ConcatDataLoader
   dataloaders.DataSplitter
   dataloaders.SemiSupervisedDataLoader
   dataloaders.SemiSupervisedDataSplitter
   dataloaders.BatchDistributedSampler
   dataloaders.MappedCollectionDataModule
   dataloaders.TileDBDataModule

Distributions

.. currentmodule:: scvi

Parameterizable probability distributions.

.. autosummary::
   :toctree: reference/
   :nosignatures:

   distributions.Poisson
   distributions.NegativeBinomial
   distributions.NegativeBinomialMixture
   distributions.ZeroInflatedNegativeBinomial
   distributions.BetaBinomial
   distributions.Normal
   distributions.Log1pNormal
   distributions.ZeroInflatedLogNormal
   distributions.ZeroInflatedGamma

Model (Base)

.. currentmodule:: scvi

These classes should be used to construct user-facing model classes.

.. autosummary::
    :toctree: reference/
    :nosignatures:

    model.base.BaseModelClass
    model.base.BaseMinifiedModeModelClass
    model.base.VAEMixin
    model.base.RNASeqMixin
    model.base.ArchesMixin
    model.base.UnsupervisedTrainingMixin
    model.base.SemisupervisedTrainingMixin
    model.base.PyroSviTrainMixin
    model.base.PyroSampleMixin
    model.base.PyroJitGuideWarmup
    model.base.PyroModelGuideWarmup
    model.base.DifferentialComputation
    model.base.EmbeddingMixin

Module

.. currentmodule:: scvi

Existing module classes with respective generative and inference procedures.

.. autosummary::
   :toctree: reference/
   :template: class_no_inherited.rst
   :nosignatures:

   module.AutoZIVAE
   module.Classifier
   module.LDVAE
   module.MRDeconv
   module.PEAKVAE
   module.MULTIVAE
   module.SCANVAE
   module.TOTALVAE
   module.VAE
   module.VAEC
   module.AmortizedLDAPyroModule

External module

.. currentmodule:: scvi

Module classes in the external API with respective generative and inference procedures.

.. autosummary::
   :toctree: reference/
   :template: class_no_inherited.rst
   :nosignatures:

   external.gimvi.JVAE
   external.cytovi.CytoVAE
   external.cellassign.CellAssignModule
   external.contrastivevi.ContrastiveDataSplitter
   external.stereoscope.RNADeconv
   external.stereoscope.SpatialDeconv
   external.scbasset.ScBassetModule
   external.contrastivevi.ContrastiveVAE
   external.velovi.VELOVAE
   external.mrvi.MRVAE
   external.mrvi_torch.TorchMRVAE
   external.methylvi.METHYLVAE
   external.methylvi.METHYLANVAE
   external.decipher.DecipherPyroModule
   external.resolvi.RESOLVAE
   external.totalanvi.TOTALANVAE
   external.scviva.nicheVAE
   external.scviva.NicheLossOutput
   external.sysvi.SysVAE
   external.diagvi.DIAGVAE

Module (Base)

.. currentmodule:: scvi

These classes should be used to construct module classes that define generative models and inference schemes.

.. autosummary::
   :toctree: reference/
   :template: class_no_inherited.rst
   :nosignatures:

   module.base.BaseModuleClass
   module.base.BaseMinifiedModeModuleClass
   module.base.SupervisedModuleClass
   module.base.PyroBaseModuleClass
   module.base.EmbeddingModuleMixin
   module.base.LossOutput
   module.base.auto_move_data

Neural networks

.. currentmodule:: scvi

Basic neural network building blocks.

.. autosummary::
   :toctree: reference/
   :template: class_no_inherited.rst
   :nosignatures:

   nn.FCLayers
   nn.Encoder
   nn.Decoder
   nn.DecoderSCVI
   nn.LinearDecoderSCVI
   nn.one_hot
   nn.Embedding
   nn.DecoderTOTALVI
   nn.EncoderTOTALVI

Train

.. currentmodule:: scvi

TrainingPlans define train/test/val optimization steps for modules.

.. autosummary::
   :toctree: reference/
   :template: class_no_inherited.rst
   :nosignatures:

   train.AdversarialTrainingPlan
   train.ClassifierTrainingPlan
   train.SemiSupervisedTrainingPlan
   train.SemiSupervisedAdversarialTrainingPlan
   train.LowLevelPyroTrainingPlan
   train.PyroTrainingPlan
   train.Trainer
   train.TrainingPlan
   train.TrainRunner
   train.ScibCallback
   train.SaveCheckpoint
   train.LoudEarlyStopping

Utilities

.. currentmodule:: scvi

Utility functions used by scvi-tools.

.. autosummary::
   :toctree: reference/
   :nosignatures:

   utils.track
   utils.setup_anndata_dsp
   utils.attrdict
   model.get_max_epochs_heuristic
   external.decipher.utils.Trajectory