Developer

Import scvi-tools as:

import scvi

Data Registration

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.

data.AnnDataManager	Provides an interface to validate and process an AnnData object for use in scvi-tools.
data.fields.BaseAnnDataField	Abstract class for a single AnnData/MuData field.
data.fields.LayerField	An AnnDataField for layer or X attributes in the AnnData data structure.
data.fields.CategoricalObsField	An AnnDataField for categorical .obs attributes in the AnnData data structure.
data.fields.NumericalJointObsField	An AnnDataField for a collection of numerical .obs fields in the AnnData data structure.
data.fields.CategoricalJointObsField	An AnnDataField for a collection of categorical .obs fields in the AnnData data structure.
data.fields.ObsmField	An AnnDataField for an .obsm field in the AnnData data structure.
data.fields.ProteinObsmField	An AnnDataField for an protein data stored in an .obsm field of an AnnData object.
data.fields.StringUnsField	An AnnDataField for string .uns attributes in the AnnData data structure.
data.fields.LabelsWithUnlabeledObsField	An AnnDataField for labels which include explicitly unlabeled cells.
data.fields.BaseMuDataWrapperClass	A wrapper class that adds MuData support for an AnnDataField.
data.fields.MuDataWrapper	Wraps an AnnDataField with BaseMuDataWrapperClass.
data.fields.MuDataLayerField
data.fields.MuDataProteinLayerField
data.fields.MuDataNumericalObsField
data.fields.MuDataCategoricalObsField
data.fields.MuDataObsmField
data.fields.MuDataNumericalJointObsField
data.fields.MuDataCategoricalJointObsField

Data Loaders

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

dataloaders.AnnDataLoader	DataLoader for loading tensors from AnnData objects.
dataloaders.AnnTorchDataset	Extension of torch dataset to get tensors from anndata.
dataloaders.ConcatDataLoader	DataLoader that supports a list of list of indices to load.
dataloaders.DataSplitter	Creates data loaders train_set, validation_set, test_set.
dataloaders.SemiSupervisedDataLoader	DataLoader that supports semisupervised training.
dataloaders.SemiSupervisedDataSplitter	Creates data loaders train_set, validation_set, test_set.

Distributions

Parameterizable probability distributions.

distributions.NegativeBinomial	Negative binomial distribution.
distributions.NegativeBinomialMixture	Negative binomial mixture distribution.
distributions.ZeroInflatedNegativeBinomial	Zero-inflated negative binomial distribution.
distributions.JaxNegativeBinomialMeanDisp	Negative binomial parameterized by mean and inverse dispersion.

Model (Base)

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

model.base.BaseModelClass	Abstract class for scvi-tools models.
model.base.BaseLatentModeModelClass	Abstract base class for scvi-tools models that support latent mode.
model.base.VAEMixin	Univseral VAE methods.
model.base.RNASeqMixin	General purpose methods for RNA-seq analysis.
model.base.ArchesMixin	Universal scArches implementation.
model.base.UnsupervisedTrainingMixin	General purpose unsupervised train method.
model.base.PyroSviTrainMixin	Mixin class for training Pyro models.
model.base.PyroSampleMixin	Mixin class for generating samples from posterior distribution.
model.base.PyroJitGuideWarmup	A callback to warmup a Pyro guide.
model.base.DifferentialComputation	Unified class for differential computation.

Module

Existing module classes with respective generative and inference procedures.

module.AutoZIVAE	Implementation of the AutoZI model [Clivio et al., 2019].
module.Classifier	Basic fully-connected NN classifier.
module.LDVAE	Linear-decoded Variational auto-encoder model.
module.MRDeconv	Model for multi-resolution deconvolution of spatial transriptomics.
module.PEAKVAE	Variational auto-encoder model for ATAC-seq data.
module.MULTIVAE	Variational auto-encoder model for joint paired + unpaired RNA-seq and ATAC-seq data.
module.SCANVAE	Single-cell annotation using variational inference.
module.TOTALVAE	Total variational inference for CITE-seq data.
module.VAE	Variational auto-encoder model.
module.VAEC	Conditional Variational auto-encoder model.
module.AmortizedLDAPyroModule	An amortized implementation of Latent Dirichlet Allocation [Blei et al., 2003] implemented in Pyro.
module.JaxVAE	Variational autoencoder model.

External module

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

external.gimvi.JVAE	Joint variational auto-encoder for imputing missing genes in spatial data.
external.cellassign.CellAssignModule	Model for CellAssign.
external.stereoscope.RNADeconv	Model of single-cell RNA-sequencing data for deconvolution of spatial transriptomics.
external.stereoscope.SpatialDeconv	Model of single-cell RNA-sequencing data for deconvolution of spatial transriptomics.

Module (Base)

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

module.base.BaseModuleClass	Abstract class for scvi-tools modules.
module.base.BaseLatentModeModuleClass	Abstract base class for scvi-tools modules that support latent mode.
module.base.PyroBaseModuleClass	Base module class for Pyro models.
module.base.JaxModuleWrapper	Wrapper class for Flax (Jax-backed) modules used to interact with model classes.
module.base.LossRecorder	Loss signature for models.
module.base.auto_move_data	Decorator for Module methods to move data to correct device.

Neural networks

Basic neural network building blocks.

nn.FCLayers	A helper class to build fully-connected layers for a neural network.
nn.Encoder	Encode data of n_input dimensions into a latent space of n_output dimensions.
nn.Decoder	Decodes data from latent space to data space.
nn.one_hot	One hot a tensor of categories.

Train

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

train.AdversarialTrainingPlan	Train vaes with adversarial loss option to encourage latent space mixing.
train.SemiSupervisedTrainingPlan	Lightning module task for SemiSupervised Training.
train.PyroTrainingPlan	Lightning module task to train Pyro scvi-tools modules.
train.JaxTrainingPlan	Lightning module task to train Pyro scvi-tools modules.
train.Trainer	Lightweight wrapper of Pytorch Lightning Trainer.
train.TrainingPlan	Lightning module task to train scvi-tools modules.
train.TrainRunner	TrainRunner calls Trainer.fit() and handles pre and post training procedures.
train.SaveBestState	Save the best module state and restore into model.
train.LoudEarlyStopping	Wrapper of Pytorch Lightning EarlyStopping callback that prints the reason for stopping on teardown.

Utilities

Utility functions used by scvi-tools.

utils.track	Progress bar with 'rich' and 'tqdm' styles.
utils.setup_anndata_dsp	A derived class of the DocstringProcessor class which provides useful parameters for the documentation of setup_anndata methods.
utils.attrdict	A dictionary that allows for attribute-style access.