Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | Z A adata (scvi.external.CellAssign attribute) (scvi.external.GIMVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.model.AmortizedLDA attribute) (scvi.model.AUTOZI attribute) (scvi.model.base.BaseLatentModeModelClass attribute) (scvi.model.base.BaseModelClass attribute) (scvi.model.CondSCVI attribute) (scvi.model.DestVI attribute) (scvi.model.JaxSCVI attribute) (scvi.model.LinearSCVI attribute) (scvi.model.MULTIVI attribute) (scvi.model.PEAKVI attribute) (scvi.model.SCANVI attribute) (scvi.model.SCVI attribute) (scvi.model.TOTALVI attribute) adata_field (scvi.data.fields.BaseMuDataWrapperClass attribute) (scvi.data.fields.MuDataCategoricalJointObsField attribute) (scvi.data.fields.MuDataCategoricalObsField attribute) (scvi.data.fields.MuDataLayerField attribute) (scvi.data.fields.MuDataNumericalJointObsField attribute) (scvi.data.fields.MuDataNumericalObsField attribute) (scvi.data.fields.MuDataObsmField attribute) (scvi.data.fields.MuDataProteinLayerField attribute) adata_manager (scvi.external.CellAssign attribute) (scvi.external.GIMVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.model.AmortizedLDA attribute) (scvi.model.AUTOZI attribute) (scvi.model.base.BaseLatentModeModelClass attribute) (scvi.model.base.BaseModelClass attribute) (scvi.model.CondSCVI attribute) (scvi.model.DestVI attribute) (scvi.model.JaxSCVI attribute) (scvi.model.LinearSCVI attribute) (scvi.model.MULTIVI attribute) (scvi.model.PEAKVI attribute) (scvi.model.SCANVI attribute) (scvi.model.SCVI attribute) (scvi.model.TOTALVI attribute) adata_uuid (scvi.data.AnnDataManager attribute) add_argparse_args() (scvi.dataloaders.DataSplitter class method) (scvi.dataloaders.SemiSupervisedDataSplitter class method) AdversarialTrainingPlan (class in scvi.train) AmortizedLDA (class in scvi.model) AmortizedLDAPyroModule (class in scvi.module) AnnDataLoader (class in scvi.dataloaders) AnnDataManager (class in scvi.data) AnnTorchDataset (class in scvi.dataloaders) apply (scvi.module.base.JaxModuleWrapper attribute) ArchesMixin (class in scvi.model.base) arg_constraints (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) as_configdict() (scvi.utils.attrdict method) attr_key (scvi.data.fields.BaseAnnDataField attribute) (scvi.data.fields.BaseMuDataWrapperClass attribute) (scvi.data.fields.CategoricalJointObsField attribute) (scvi.data.fields.CategoricalObsField attribute) (scvi.data.fields.LabelsWithUnlabeledObsField attribute) (scvi.data.fields.LayerField attribute) (scvi.data.fields.MuDataCategoricalJointObsField attribute) (scvi.data.fields.MuDataCategoricalObsField attribute) (scvi.data.fields.MuDataLayerField attribute) (scvi.data.fields.MuDataNumericalJointObsField attribute) (scvi.data.fields.MuDataNumericalObsField attribute) (scvi.data.fields.MuDataObsmField attribute) (scvi.data.fields.MuDataProteinLayerField attribute) (scvi.data.fields.NumericalJointObsField attribute) (scvi.data.fields.ObsmField attribute) (scvi.data.fields.ProteinObsmField attribute) (scvi.data.fields.StringUnsField attribute) attr_name (scvi.data.fields.BaseAnnDataField attribute) (scvi.data.fields.BaseMuDataWrapperClass attribute) (scvi.data.fields.CategoricalJointObsField attribute) (scvi.data.fields.CategoricalObsField attribute) (scvi.data.fields.LabelsWithUnlabeledObsField attribute) (scvi.data.fields.LayerField attribute) (scvi.data.fields.MuDataCategoricalJointObsField attribute) (scvi.data.fields.MuDataCategoricalObsField attribute) (scvi.data.fields.MuDataLayerField attribute) (scvi.data.fields.MuDataNumericalJointObsField attribute) (scvi.data.fields.MuDataNumericalObsField attribute) (scvi.data.fields.MuDataObsmField attribute) (scvi.data.fields.MuDataProteinLayerField attribute) (scvi.data.fields.NumericalJointObsField attribute) (scvi.data.fields.ObsmField attribute) (scvi.data.fields.ProteinObsmField attribute) (scvi.data.fields.StringUnsField attribute) attrdict (class in scvi.utils) auto_move_data (class in scvi.module.base) AUTOZI (class in scvi.model) AutoZIVAE (class in scvi.module) B backward() (scvi.train.JaxTrainingPlan method) (scvi.train.PyroTrainingPlan method) BaseAnnDataField (class in scvi.data.fields) BaseLatentModeModelClass (class in scvi.model.base) BaseLatentModeModuleClass (class in scvi.module.base) BaseModelClass (class in scvi.model.base) BaseModuleClass (class in scvi.module.base) BaseMuDataWrapperClass (class in scvi.data.fields) batch_shape (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) batch_size (scvi._settings.ScviConfig attribute) (scvi.dataloaders.AnnDataLoader attribute) (scvi.dataloaders.ConcatDataLoader attribute) (scvi.dataloaders.SemiSupervisedDataLoader attribute) brainlarge_dataset() (in module scvi.data) breast_cancer_dataset() (in module scvi.data) C CATEGORICAL_MAPPING_KEY (scvi.data.fields.CategoricalObsField attribute) (scvi.data.fields.LabelsWithUnlabeledObsField attribute) CategoricalJointObsField (class in scvi.data.fields) CategoricalObsField (class in scvi.data.fields) cdf() (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.ZeroInflatedNegativeBinomial method) CellAssign (class in scvi.external) CellAssignModule (class in scvi.external.cellassign) check_monitor_top() (scvi.train.SaveBestState method) check_worker_number_rationality() (scvi.dataloaders.AnnDataLoader method) (scvi.dataloaders.ConcatDataLoader method) (scvi.dataloaders.SemiSupervisedDataLoader method) CHECKPOINT_HYPER_PARAMS_KEY (scvi.dataloaders.DataSplitter attribute) (scvi.dataloaders.SemiSupervisedDataSplitter attribute) CHECKPOINT_HYPER_PARAMS_NAME (scvi.dataloaders.DataSplitter attribute) (scvi.dataloaders.SemiSupervisedDataSplitter attribute) CHECKPOINT_HYPER_PARAMS_TYPE (scvi.dataloaders.DataSplitter attribute) (scvi.dataloaders.SemiSupervisedDataSplitter attribute) classification_loss() (scvi.module.SCANVAE method) Classifier (class in scvi.module) classify() (scvi.module.SCANVAE method) COLUMN_NAMES_KEY (scvi.data.fields.LayerField attribute) (scvi.data.fields.ObsmField attribute) (scvi.data.fields.ProteinObsmField attribute) COLUMNS_KEY (scvi.data.fields.NumericalJointObsField attribute) compute_and_log_metrics() (scvi.train.TrainingPlan method) compute_global_kl_divergence() (scvi.module.AutoZIVAE method) ConcatDataLoader (class in scvi.dataloaders) CondSCVI (class in scvi.model) configure_optimizers() (scvi.train.AdversarialTrainingPlan method) (scvi.train.JaxTrainingPlan method) (scvi.train.PyroTrainingPlan method) (scvi.train.TrainingPlan method) convert_dict (scvi.utils.attrdict attribute) convert_legacy_save() (scvi.external.CellAssign class method) (scvi.external.GIMVI class method) (scvi.external.RNAStereoscope class method) (scvi.external.SCAR class method) (scvi.external.SOLO class method) (scvi.external.SpatialStereoscope class method) (scvi.model.AmortizedLDA class method) (scvi.model.AUTOZI class method) (scvi.model.base.BaseLatentModeModelClass class method) (scvi.model.base.BaseModelClass class method) (scvi.model.CondSCVI class method) (scvi.model.DestVI class method) (scvi.model.JaxSCVI class method) (scvi.model.LinearSCVI class method) (scvi.model.MULTIVI class method) (scvi.model.PEAKVI class method) (scvi.model.SCANVI class method) (scvi.model.SCVI class method) (scvi.model.TOTALVI class method) copy_and_resolve_references() (scvi.utils.attrdict method) cortex() (in module scvi.data) create_doublets() (scvi.external.SOLO class method) create_predictive() (scvi.module.base.PyroBaseModuleClass method) D data_registry (scvi.data.AnnDataManager attribute) dataset (scvi.dataloaders.AnnDataLoader attribute) (scvi.dataloaders.ConcatDataLoader attribute) (scvi.dataloaders.SemiSupervisedDataLoader attribute) dataset_10x() (in module scvi.data) DataSplitter (class in scvi.dataloaders) Decoder (class in scvi.nn) DestVI (class in scvi.model) device (scvi.external.CellAssign attribute) (scvi.external.GIMVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.model.AmortizedLDA attribute) (scvi.model.AUTOZI attribute) (scvi.model.base.BaseLatentModeModelClass attribute) (scvi.model.base.BaseModelClass attribute) (scvi.model.CondSCVI attribute) (scvi.model.DestVI attribute) (scvi.model.JaxSCVI attribute) (scvi.model.LinearSCVI attribute) (scvi.model.MULTIVI attribute) (scvi.model.PEAKVI attribute) (scvi.model.SCANVI attribute) (scvi.model.SCVI attribute) (scvi.model.TOTALVI attribute) (scvi.module.base.BaseModuleClass attribute) (scvi.module.base.JaxModuleWrapper attribute) differential_accessibility() (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) differential_expression() (scvi.external.SCAR method) (scvi.model.base.RNASeqMixin method) (scvi.model.CondSCVI method) (scvi.model.LinearSCVI method) (scvi.model.MULTIVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) DifferentialComputation (class in scvi.model.base) dl_num_workers (scvi._settings.ScviConfig attribute) dl_pin_memory_gpu_training (scvi._settings.ScviConfig attribute) drop_last (scvi.dataloaders.AnnDataLoader attribute) (scvi.dataloaders.ConcatDataLoader attribute) (scvi.dataloaders.SemiSupervisedDataLoader attribute) dropout_rate (scvi.module.JaxVAE attribute) E Encoder (class in scvi.nn) entropy() (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.ZeroInflatedNegativeBinomial method) enumerate_support() (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.ZeroInflatedNegativeBinomial method) eps (scvi.module.JaxVAE attribute) eq_as_configdict() (scvi.utils.attrdict method) eval() (scvi.module.base.JaxModuleWrapper method) event_dim (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) event_shape (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) expand() (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.ZeroInflatedNegativeBinomial method) expand_by() (scvi.distributions.JaxNegativeBinomialMeanDisp method) F FCLayers (class in scvi.nn) FIELD_KEYS_KEY (scvi.data.fields.CategoricalJointObsField attribute) fit() (scvi.train.Trainer method) forward() (scvi.module.base.BaseModuleClass method) (scvi.module.base.PyroBaseModuleClass method) (scvi.module.Classifier method) (scvi.nn.Decoder method) (scvi.nn.Encoder method) (scvi.nn.FCLayers method) (scvi.train.JaxTrainingPlan method) (scvi.train.PyroTrainingPlan method) (scvi.train.TrainingPlan method) from_argparse_args() (scvi.dataloaders.DataSplitter class method) (scvi.dataloaders.SemiSupervisedDataSplitter class method) from_datasets() (scvi.dataloaders.DataSplitter class method) (scvi.dataloaders.SemiSupervisedDataSplitter class method) from_rna_model() (scvi.external.SpatialStereoscope class method) (scvi.model.DestVI class method) from_scvi_model() (scvi.external.SOLO class method) (scvi.model.SCANVI class method) frontalcortex_dropseq() (in module scvi.data) G gene_likelihood (scvi.module.JaxVAE attribute) generative() (scvi.external.cellassign.CellAssignModule method) (scvi.external.gimvi.JVAE method) (scvi.external.stereoscope.RNADeconv method) (scvi.external.stereoscope.SpatialDeconv method) (scvi.module.AutoZIVAE method) (scvi.module.base.BaseModuleClass method) (scvi.module.JaxVAE method) (scvi.module.MRDeconv method) (scvi.module.MULTIVAE method) (scvi.module.PEAKVAE method) (scvi.module.TOTALVAE method) (scvi.module.VAE method) (scvi.module.VAEC method) get() (scvi.utils.attrdict method) get_accessibility_estimates() (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) get_alphas_betas() (scvi.model.AUTOZI method) (scvi.module.AutoZIVAE method) get_ambient_profile() (scvi.external.SCAR static method) get_anndata_manager() (scvi.external.CellAssign method) (scvi.external.GIMVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.model.AmortizedLDA method) (scvi.model.AUTOZI method) (scvi.model.base.BaseLatentModeModelClass method) (scvi.model.base.BaseModelClass method) (scvi.model.CondSCVI method) (scvi.model.DestVI method) (scvi.model.JaxSCVI method) (scvi.model.LinearSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) get_bayes_factors() (scvi.model.base.DifferentialComputation method) get_ct_specific_expression() (scvi.external.stereoscope.SpatialDeconv method) (scvi.module.MRDeconv method) get_data() (scvi.dataloaders.AnnTorchDataset method) get_data_registry() (scvi.data.fields.BaseAnnDataField method) (scvi.data.fields.BaseMuDataWrapperClass method) (scvi.data.fields.CategoricalJointObsField method) (scvi.data.fields.CategoricalObsField method) (scvi.data.fields.LabelsWithUnlabeledObsField method) (scvi.data.fields.LayerField method) (scvi.data.fields.MuDataCategoricalJointObsField method) (scvi.data.fields.MuDataCategoricalObsField method) (scvi.data.fields.MuDataLayerField method) (scvi.data.fields.MuDataNumericalJointObsField method) (scvi.data.fields.MuDataNumericalObsField method) (scvi.data.fields.MuDataObsmField method) (scvi.data.fields.MuDataProteinLayerField method) (scvi.data.fields.NumericalJointObsField method) (scvi.data.fields.ObsmField method) (scvi.data.fields.ProteinObsmField method) (scvi.data.fields.StringUnsField method) get_denoised_counts() (scvi.external.SCAR method) get_elbo() (scvi.external.GIMVI method) (scvi.external.SCAR method) (scvi.model.AmortizedLDA method) (scvi.model.AUTOZI method) (scvi.model.base.VAEMixin method) (scvi.model.CondSCVI method) (scvi.model.LinearSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) (scvi.module.AmortizedLDAPyroModule method) get_feature_by_topic() (scvi.model.AmortizedLDA method) get_feature_correlation_matrix() (scvi.external.SCAR method) (scvi.model.base.RNASeqMixin method) (scvi.model.CondSCVI method) (scvi.model.LinearSCVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) get_field_data() (scvi.data.fields.BaseAnnDataField method) (scvi.data.fields.BaseMuDataWrapperClass method) (scvi.data.fields.CategoricalJointObsField method) (scvi.data.fields.CategoricalObsField method) (scvi.data.fields.LabelsWithUnlabeledObsField method) (scvi.data.fields.LayerField method) (scvi.data.fields.MuDataCategoricalJointObsField method) (scvi.data.fields.MuDataCategoricalObsField method) (scvi.data.fields.MuDataLayerField method) (scvi.data.fields.MuDataNumericalJointObsField method) (scvi.data.fields.MuDataNumericalObsField method) (scvi.data.fields.MuDataObsmField method) (scvi.data.fields.MuDataProteinLayerField method) (scvi.data.fields.NumericalJointObsField method) (scvi.data.fields.ObsmField method) (scvi.data.fields.ProteinObsmField method) (scvi.data.fields.StringUnsField method) get_from_registry() (scvi.data.AnnDataManager method) (scvi.external.CellAssign method) (scvi.external.GIMVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.model.AmortizedLDA method) (scvi.model.AUTOZI method) (scvi.model.base.BaseLatentModeModelClass method) (scvi.model.base.BaseModelClass method) (scvi.model.CondSCVI method) (scvi.model.DestVI method) (scvi.model.JaxSCVI method) (scvi.model.LinearSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) get_gamma() (scvi.model.DestVI method) (scvi.module.MRDeconv method) get_imputed_values() (scvi.external.GIMVI method) get_inference_fn() (scvi.module.base.JaxModuleWrapper method) get_init_arguments_and_types() (scvi.dataloaders.DataSplitter class method) (scvi.dataloaders.SemiSupervisedDataSplitter class method) get_latent_library_size() (scvi.external.SCAR method) (scvi.model.base.RNASeqMixin method) (scvi.model.CondSCVI method) (scvi.model.LinearSCVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) get_latent_representation() (scvi.external.GIMVI method) (scvi.external.SCAR method) (scvi.model.AmortizedLDA method) (scvi.model.AUTOZI method) (scvi.model.base.VAEMixin method) (scvi.model.CondSCVI method) (scvi.model.JaxSCVI method) (scvi.model.LinearSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) get_library_size_factors() (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) get_likelihood_parameters() (scvi.external.SCAR method) (scvi.model.base.RNASeqMixin method) (scvi.model.CondSCVI method) (scvi.model.LinearSCVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) get_loadings() (scvi.model.LinearSCVI method) (scvi.module.LDVAE method) get_marginal_ll() (scvi.external.GIMVI method) (scvi.external.SCAR method) (scvi.model.AUTOZI method) (scvi.model.base.VAEMixin method) (scvi.model.CondSCVI method) (scvi.model.LinearSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) get_modality() (scvi.data.fields.BaseMuDataWrapperClass method) (scvi.data.fields.MuDataCategoricalJointObsField method) (scvi.data.fields.MuDataCategoricalObsField method) (scvi.data.fields.MuDataLayerField method) (scvi.data.fields.MuDataNumericalJointObsField method) (scvi.data.fields.MuDataNumericalObsField method) (scvi.data.fields.MuDataObsmField method) (scvi.data.fields.MuDataProteinLayerField method) get_normalized_expression() (scvi.external.SCAR method) (scvi.model.base.RNASeqMixin method) (scvi.model.CondSCVI method) (scvi.model.LinearSCVI method) (scvi.model.MULTIVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) get_oneway_ref() (scvi.utils.attrdict method) get_params() (scvi.external.stereoscope.RNADeconv method) get_perplexity() (scvi.model.AmortizedLDA method) get_proportions() (scvi.external.SpatialStereoscope method) (scvi.external.stereoscope.SpatialDeconv method) (scvi.model.DestVI method) (scvi.module.MRDeconv method) get_protein_background_mean() (scvi.model.TOTALVI method) get_protein_foreground_probability() (scvi.model.MULTIVI method) (scvi.model.TOTALVI method) get_reconstruction_error() (scvi.external.GIMVI method) (scvi.external.SCAR method) (scvi.model.AUTOZI method) (scvi.model.base.VAEMixin method) (scvi.model.CondSCVI method) (scvi.model.LinearSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) get_reconstruction_loss() (scvi.module.AutoZIVAE method) (scvi.module.PEAKVAE method) (scvi.module.TOTALVAE method) get_reconstruction_loss_accessibility() (scvi.module.MULTIVAE method) get_reconstruction_loss_expression() (scvi.module.MULTIVAE method) get_ref() (scvi.utils.attrdict method) get_region_factors() (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) get_sample_dispersion() (scvi.module.TOTALVAE method) get_sample_rate() (scvi.external.gimvi.JVAE method) get_scale_for_ct() (scvi.external.SpatialStereoscope method) (scvi.model.DestVI method) get_state_registry() (scvi.data.AnnDataManager method) get_summary_stats() (scvi.data.fields.BaseAnnDataField method) (scvi.data.fields.BaseMuDataWrapperClass method) (scvi.data.fields.CategoricalJointObsField method) (scvi.data.fields.CategoricalObsField method) (scvi.data.fields.LabelsWithUnlabeledObsField method) (scvi.data.fields.LayerField method) (scvi.data.fields.MuDataCategoricalJointObsField method) (scvi.data.fields.MuDataCategoricalObsField method) (scvi.data.fields.MuDataLayerField method) (scvi.data.fields.MuDataNumericalJointObsField method) (scvi.data.fields.MuDataNumericalObsField method) (scvi.data.fields.MuDataObsmField method) (scvi.data.fields.MuDataProteinLayerField method) (scvi.data.fields.NumericalJointObsField method) (scvi.data.fields.ObsmField method) (scvi.data.fields.ProteinObsmField method) (scvi.data.fields.StringUnsField method) get_topic_distribution() (scvi.module.AmortizedLDAPyroModule method) get_type() (scvi.utils.attrdict method) get_vamp_prior() (scvi.model.CondSCVI method) GIMVI (class in scvi.external) guide (scvi.module.AmortizedLDAPyroModule attribute) (scvi.module.base.PyroBaseModuleClass attribute) H has_enumerate_support (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) has_rsample (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) heart_cell_atlas_subsampled() (in module scvi.data) history (scvi.external.CellAssign attribute) (scvi.external.GIMVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.model.AmortizedLDA attribute) (scvi.model.AUTOZI attribute) (scvi.model.base.BaseLatentModeModelClass attribute) (scvi.model.base.BaseModelClass attribute) (scvi.model.CondSCVI attribute) (scvi.model.DestVI attribute) (scvi.model.JaxSCVI attribute) (scvi.model.LinearSCVI attribute) (scvi.model.MULTIVI attribute) (scvi.model.PEAKVI attribute) (scvi.model.SCANVI attribute) (scvi.model.SCVI attribute) (scvi.model.TOTALVI attribute) hparams (scvi.dataloaders.DataSplitter attribute) (scvi.dataloaders.SemiSupervisedDataSplitter attribute) hparams_initial (scvi.dataloaders.DataSplitter attribute) (scvi.dataloaders.SemiSupervisedDataSplitter attribute) I icdf() (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.ZeroInflatedNegativeBinomial method) ignore_type() (scvi.utils.attrdict method) infer_shapes() (scvi.distributions.JaxNegativeBinomialMeanDisp class method) inference() (scvi.external.cellassign.CellAssignModule method) (scvi.external.gimvi.JVAE method) (scvi.external.stereoscope.RNADeconv method) (scvi.external.stereoscope.SpatialDeconv method) (scvi.module.base.BaseLatentModeModuleClass method) (scvi.module.base.BaseModuleClass method) (scvi.module.JaxVAE method) (scvi.module.MRDeconv method) (scvi.module.MULTIVAE method) (scvi.module.PEAKVAE method) (scvi.module.TOTALVAE method) (scvi.module.VAEC method) init (scvi.module.base.JaxModuleWrapper attribute) initialize_train_metrics() (scvi.train.TrainingPlan method) initialize_val_metrics() (scvi.train.TrainingPlan method) inject_into_layer() (scvi.nn.FCLayers method) inverse_dispersion (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) is_discrete (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) is_empty (scvi.data.fields.BaseAnnDataField attribute) (scvi.data.fields.BaseMuDataWrapperClass attribute) (scvi.data.fields.CategoricalJointObsField attribute) (scvi.data.fields.CategoricalObsField attribute) (scvi.data.fields.LabelsWithUnlabeledObsField attribute) (scvi.data.fields.LayerField attribute) (scvi.data.fields.MuDataCategoricalJointObsField attribute) (scvi.data.fields.MuDataCategoricalObsField attribute) (scvi.data.fields.MuDataLayerField attribute) (scvi.data.fields.MuDataNumericalJointObsField attribute) (scvi.data.fields.MuDataNumericalObsField attribute) (scvi.data.fields.MuDataObsmField attribute) (scvi.data.fields.MuDataProteinLayerField attribute) (scvi.data.fields.NumericalJointObsField attribute) (scvi.data.fields.ObsmField attribute) (scvi.data.fields.ProteinObsmField attribute) (scvi.data.fields.StringUnsField attribute) is_locked (scvi.utils.attrdict attribute) is_trained (scvi.external.CellAssign attribute) (scvi.external.GIMVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.model.AmortizedLDA attribute) (scvi.model.AUTOZI attribute) (scvi.model.base.BaseLatentModeModelClass attribute) (scvi.model.base.BaseModelClass attribute) (scvi.model.CondSCVI attribute) (scvi.model.DestVI attribute) (scvi.model.JaxSCVI attribute) (scvi.model.LinearSCVI attribute) (scvi.model.MULTIVI attribute) (scvi.model.PEAKVI attribute) (scvi.model.SCANVI attribute) (scvi.model.SCVI attribute) (scvi.model.TOTALVI attribute) is_type_safe (scvi.utils.attrdict attribute) items() (scvi.utils.attrdict method) iteritems() (scvi.utils.attrdict method) iterkeys() (scvi.utils.attrdict method) itervalues() (scvi.utils.attrdict method) J jax_preallocate_gpu_memory (scvi._settings.ScviConfig attribute) JaxModuleWrapper (class in scvi.module.base) JaxNegativeBinomialMeanDisp (class in scvi.distributions) JaxSCVI (class in scvi.model) JaxTrainingPlan (class in scvi.train) JaxVAE (class in scvi.module) jit_training_step() (scvi.train.JaxTrainingPlan static method) jit_validation_step() (scvi.train.JaxTrainingPlan method) JVAE (class in scvi.external.gimvi) K keys() (scvi.utils.attrdict method) kl_global (scvi.module.base.LossRecorder attribute) kl_local (scvi.module.base.LossRecorder attribute) kl_weight (scvi.train.JaxTrainingPlan attribute) (scvi.train.PyroTrainingPlan attribute) (scvi.train.TrainingPlan attribute) L LabelsWithUnlabeledObsField (class in scvi.data.fields) latent_data_type (scvi.model.base.BaseLatentModeModelClass attribute) (scvi.model.SCVI attribute) (scvi.module.base.BaseLatentModeModuleClass attribute) LayerField (class in scvi.data.fields) LDVAE (class in scvi.module) LinearSCVI (class in scvi.model) list_obs_plate_vars (scvi.module.base.PyroBaseModuleClass attribute) load() (scvi.external.CellAssign class method) (scvi.external.GIMVI class method) (scvi.external.RNAStereoscope class method) (scvi.external.SCAR class method) (scvi.external.SOLO class method) (scvi.external.SpatialStereoscope class method) (scvi.model.AmortizedLDA class method) (scvi.model.AUTOZI class method) (scvi.model.base.BaseLatentModeModelClass class method) (scvi.model.base.BaseModelClass class method) (scvi.model.CondSCVI class method) (scvi.model.DestVI class method) (scvi.model.JaxSCVI class method) (scvi.model.LinearSCVI class method) (scvi.model.MULTIVI class method) (scvi.model.PEAKVI class method) (scvi.model.SCANVI class method) (scvi.model.SCVI class method) (scvi.model.TOTALVI class method) load_from_checkpoint() (scvi.dataloaders.DataSplitter class method) (scvi.dataloaders.SemiSupervisedDataSplitter class method) load_query_data() (scvi.model.base.ArchesMixin class method) (scvi.model.MULTIVI class method) (scvi.model.PEAKVI class method) (scvi.model.SCANVI class method) (scvi.model.SCVI class method) (scvi.model.TOTALVI class method) load_registry() (scvi.external.CellAssign static method) (scvi.external.GIMVI static method) (scvi.external.RNAStereoscope static method) (scvi.external.SCAR static method) (scvi.external.SOLO static method) (scvi.external.SpatialStereoscope static method) (scvi.model.AmortizedLDA static method) (scvi.model.AUTOZI static method) (scvi.model.base.BaseLatentModeModelClass static method) (scvi.model.base.BaseModelClass static method) (scvi.model.CondSCVI static method) (scvi.model.DestVI static method) (scvi.model.JaxSCVI static method) (scvi.model.LinearSCVI static method) (scvi.model.MULTIVI static method) (scvi.model.PEAKVI static method) (scvi.model.SCANVI static method) (scvi.model.SCVI static method) (scvi.model.TOTALVI static method) load_state_dict() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.model.base.PyroJitGuideWarmup method) (scvi.module.base.JaxModuleWrapper method) lock() (scvi.utils.attrdict method) log_prob() (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.ZeroInflatedNegativeBinomial method) logging_dir (scvi._settings.ScviConfig attribute) loss (scvi.module.base.JaxModuleWrapper attribute) (scvi.module.base.LossRecorder attribute) loss() (scvi.external.cellassign.CellAssignModule method) (scvi.external.gimvi.JVAE method) (scvi.external.stereoscope.RNADeconv method) (scvi.external.stereoscope.SpatialDeconv method) (scvi.module.AutoZIVAE method) (scvi.module.base.BaseModuleClass method) (scvi.module.JaxVAE method) (scvi.module.MRDeconv method) (scvi.module.MULTIVAE method) (scvi.module.PEAKVAE method) (scvi.module.SCANVAE method) (scvi.module.TOTALVAE method) (scvi.module.VAE method) (scvi.module.VAEC method) loss_adversarial_classifier() (scvi.train.AdversarialTrainingPlan method) LossRecorder (class in scvi.module.base) LoudEarlyStopping (class in scvi.train) M MAPPINGS_KEY (scvi.data.fields.CategoricalJointObsField attribute) marginal_ll() (scvi.module.TOTALVAE method) (scvi.module.VAE method) mask() (scvi.distributions.JaxNegativeBinomialMeanDisp method) mde() (in module scvi.model.utils) mean (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) mixture_probs (scvi.distributions.NegativeBinomialMixture attribute) mod_key (scvi.data.fields.BaseAnnDataField attribute) (scvi.data.fields.BaseMuDataWrapperClass attribute) (scvi.data.fields.CategoricalJointObsField attribute) (scvi.data.fields.CategoricalObsField attribute) (scvi.data.fields.LabelsWithUnlabeledObsField attribute) (scvi.data.fields.LayerField attribute) (scvi.data.fields.MuDataCategoricalJointObsField attribute) (scvi.data.fields.MuDataCategoricalObsField attribute) (scvi.data.fields.MuDataLayerField attribute) (scvi.data.fields.MuDataNumericalJointObsField attribute) (scvi.data.fields.MuDataNumericalObsField attribute) (scvi.data.fields.MuDataObsmField attribute) (scvi.data.fields.MuDataProteinLayerField attribute) (scvi.data.fields.NumericalJointObsField attribute) (scvi.data.fields.ObsmField attribute) (scvi.data.fields.ProteinObsmField attribute) (scvi.data.fields.StringUnsField attribute) mode (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) model (scvi.module.AmortizedLDAPyroModule attribute) (scvi.module.base.PyroBaseModuleClass attribute) module (scvi.module.base.JaxModuleWrapper attribute) mouse_ob_dataset() (in module scvi.data) MRDeconv (class in scvi.module) MuDataCategoricalJointObsField (class in scvi.data.fields) MuDataCategoricalObsField (class in scvi.data.fields) MuDataLayerField (class in scvi.data.fields) MuDataNumericalJointObsField (class in scvi.data.fields) MuDataNumericalObsField (class in scvi.data.fields) MuDataObsmField (class in scvi.data.fields) MuDataProteinLayerField (class in scvi.data.fields) MuDataWrapper() (in module scvi.data.fields) multiprocessing_context (scvi.dataloaders.AnnDataLoader attribute) (scvi.dataloaders.ConcatDataLoader attribute) (scvi.dataloaders.SemiSupervisedDataLoader attribute) MULTIVAE (class in scvi.module) MULTIVI (class in scvi.model) N n_batch (scvi.module.JaxVAE attribute) N_CATS_PER_KEY (scvi.data.fields.CategoricalJointObsField attribute) N_CELLS_KEY (scvi.data.fields.LayerField attribute) n_hidden (scvi.module.JaxVAE attribute) n_input (scvi.module.JaxVAE attribute) n_latent (scvi.module.JaxVAE attribute) n_layers (scvi.module.JaxVAE attribute) N_OBS_KEY (scvi.data.fields.LayerField attribute) n_obs_training (scvi.train.PyroTrainingPlan attribute) (scvi.train.TrainingPlan attribute) n_obs_validation (scvi.train.TrainingPlan attribute) N_VARS_KEY (scvi.data.fields.LayerField attribute) name (scvi.dataloaders.DataSplitter attribute) (scvi.dataloaders.SemiSupervisedDataSplitter attribute) (scvi.module.JaxVAE attribute) NegativeBinomial (class in scvi.distributions) NegativeBinomialMixture (class in scvi.distributions) num_threads (scvi._settings.ScviConfig attribute) num_workers (scvi.dataloaders.AnnDataLoader attribute) (scvi.dataloaders.ConcatDataLoader attribute) (scvi.dataloaders.SemiSupervisedDataLoader attribute) NumericalJointObsField (class in scvi.data.fields) O obs_keys (scvi.data.fields.CategoricalJointObsField attribute) (scvi.data.fields.NumericalJointObsField attribute) ObsmField (class in scvi.data.fields) on_after_backward() (scvi.model.base.PyroJitGuideWarmup method) on_after_batch_transfer() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) on_batch_end() (scvi.model.base.PyroJitGuideWarmup method) on_batch_start() (scvi.model.base.PyroJitGuideWarmup method) on_before_accelerator_backend_setup() (scvi.model.base.PyroJitGuideWarmup method) on_before_backward() (scvi.model.base.PyroJitGuideWarmup method) on_before_batch_transfer() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) on_before_optimizer_step() (scvi.model.base.PyroJitGuideWarmup method) on_before_zero_grad() (scvi.model.base.PyroJitGuideWarmup method) on_configure_sharded_model() (scvi.model.base.PyroJitGuideWarmup method) on_epoch_end() (scvi.model.base.PyroJitGuideWarmup method) (scvi.train.SaveBestState method) on_epoch_start() (scvi.model.base.PyroJitGuideWarmup method) on_exception() (scvi.model.base.PyroJitGuideWarmup method) on_fit_end() (scvi.model.base.PyroJitGuideWarmup method) on_fit_start() (scvi.model.base.PyroJitGuideWarmup method) on_init_end() (scvi.model.base.PyroJitGuideWarmup method) on_init_start() (scvi.model.base.PyroJitGuideWarmup method) on_load() (scvi.module.base.BaseModuleClass method) (scvi.module.base.JaxModuleWrapper static method) (scvi.module.base.PyroBaseModuleClass method) on_load_checkpoint() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.model.base.PyroJitGuideWarmup method) on_predict_batch_end() (scvi.model.base.PyroJitGuideWarmup method) on_predict_batch_start() (scvi.model.base.PyroJitGuideWarmup method) on_predict_end() (scvi.model.base.PyroJitGuideWarmup method) on_predict_epoch_end() (scvi.model.base.PyroJitGuideWarmup method) on_predict_epoch_start() (scvi.model.base.PyroJitGuideWarmup method) on_predict_start() (scvi.model.base.PyroJitGuideWarmup method) on_pretrain_routine_end() (scvi.model.base.PyroJitGuideWarmup method) on_pretrain_routine_start() (scvi.model.base.PyroJitGuideWarmup method) on_sanity_check_end() (scvi.model.base.PyroJitGuideWarmup method) on_sanity_check_start() (scvi.model.base.PyroJitGuideWarmup method) on_save_checkpoint() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.model.base.PyroJitGuideWarmup method) on_test_batch_end() (scvi.model.base.PyroJitGuideWarmup method) on_test_batch_start() (scvi.model.base.PyroJitGuideWarmup method) on_test_end() (scvi.model.base.PyroJitGuideWarmup method) on_test_epoch_end() (scvi.model.base.PyroJitGuideWarmup method) on_test_epoch_start() (scvi.model.base.PyroJitGuideWarmup method) on_test_start() (scvi.model.base.PyroJitGuideWarmup method) on_train_batch_end() (scvi.model.base.PyroJitGuideWarmup method) on_train_batch_start() (scvi.model.base.PyroJitGuideWarmup method) on_train_end() (scvi.model.base.PyroJitGuideWarmup method) (scvi.train.SaveBestState method) on_train_epoch_end() (scvi.model.base.PyroJitGuideWarmup method) on_train_epoch_start() (scvi.model.base.PyroJitGuideWarmup method) on_train_start() (scvi.model.base.PyroJitGuideWarmup method) (scvi.train.SaveBestState method) on_validation_batch_end() (scvi.model.base.PyroJitGuideWarmup method) on_validation_batch_start() (scvi.model.base.PyroJitGuideWarmup method) on_validation_end() (scvi.model.base.PyroJitGuideWarmup method) on_validation_epoch_end() (scvi.model.base.PyroJitGuideWarmup method) on_validation_epoch_start() (scvi.model.base.PyroJitGuideWarmup method) on_validation_start() (scvi.model.base.PyroJitGuideWarmup method) one_hot (class in scvi.nn) optimizer_step() (scvi.train.JaxTrainingPlan method) (scvi.train.PyroTrainingPlan method) organize_cite_seq_10x() (in module scvi.data) organize_multiome_anndatas() (in module scvi.data) ORIGINAL_ATTR_KEY (scvi.data.fields.CategoricalObsField attribute) (scvi.data.fields.LabelsWithUnlabeledObsField attribute) P params (scvi.module.base.JaxModuleWrapper attribute) parent (scvi.module.JaxVAE attribute) pbmc_dataset() (in module scvi.data) pbmc_seurat_v4_cite_seq() (in module scvi.data) pbmcs_10x_cite_seq() (in module scvi.data) PEAKVAE (class in scvi.module) PEAKVI (class in scvi.model) perplexity() (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.ZeroInflatedNegativeBinomial method) pin_memory (scvi.dataloaders.AnnDataLoader attribute) (scvi.dataloaders.ConcatDataLoader attribute) (scvi.dataloaders.SemiSupervisedDataLoader attribute) pin_memory_device (scvi.dataloaders.AnnDataLoader attribute) (scvi.dataloaders.ConcatDataLoader attribute) (scvi.dataloaders.SemiSupervisedDataLoader attribute) poisson_gene_selection() (in module scvi.data) posterior_predictive_sample() (scvi.external.SCAR method) (scvi.model.base.RNASeqMixin method) (scvi.model.CondSCVI method) (scvi.model.LinearSCVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) predict() (scvi.external.CellAssign method) (scvi.external.SOLO method) (scvi.model.SCANVI method) predict_dataloader() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) prefetch_factor (scvi.dataloaders.AnnDataLoader attribute) (scvi.dataloaders.ConcatDataLoader attribute) (scvi.dataloaders.SemiSupervisedDataLoader attribute) prefrontalcortex_starmap() (in module scvi.data) prepare_data() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) prepare_query_anndata() (scvi.model.base.ArchesMixin static method) (scvi.model.MULTIVI static method) (scvi.model.PEAKVI static method) (scvi.model.SCANVI static method) (scvi.model.SCVI static method) (scvi.model.TOTALVI static method) preregister() (scvi.data.fields.BaseMuDataWrapperClass method) (scvi.data.fields.MuDataCategoricalJointObsField method) (scvi.data.fields.MuDataCategoricalObsField method) (scvi.data.fields.MuDataLayerField method) (scvi.data.fields.MuDataNumericalJointObsField method) (scvi.data.fields.MuDataNumericalObsField method) (scvi.data.fields.MuDataObsmField method) (scvi.data.fields.MuDataProteinLayerField method) progress_bar_style (scvi._settings.ScviConfig attribute) PROTEIN_BATCH_MASK (scvi.data.fields.ProteinObsmField attribute) ProteinObsmField (class in scvi.data.fields) purified_pbmc_dataset() (in module scvi.data) PyroBaseModuleClass (class in scvi.module.base) PyroJitGuideWarmup (class in scvi.model.base) PyroSampleMixin (class in scvi.model.base) PyroSviTrainMixin (class in scvi.model.base) PyroTrainingPlan (class in scvi.train) R read_10x_atac() (in module scvi.data) read_10x_multiome() (in module scvi.data) read_csv() (in module scvi.data) read_h5ad() (in module scvi.data) read_loom() (in module scvi.data) read_text() (in module scvi.data) reconstruction_loss (scvi.module.base.LossRecorder attribute) reconstruction_loss() (scvi.external.gimvi.JVAE method) register_field() (scvi.data.fields.BaseAnnDataField method) (scvi.data.fields.BaseMuDataWrapperClass method) (scvi.data.fields.CategoricalJointObsField method) (scvi.data.fields.CategoricalObsField method) (scvi.data.fields.LabelsWithUnlabeledObsField method) (scvi.data.fields.LayerField method) (scvi.data.fields.MuDataCategoricalJointObsField method) (scvi.data.fields.MuDataCategoricalObsField method) (scvi.data.fields.MuDataLayerField method) (scvi.data.fields.MuDataNumericalJointObsField method) (scvi.data.fields.MuDataNumericalObsField method) (scvi.data.fields.MuDataObsmField method) (scvi.data.fields.MuDataProteinLayerField method) (scvi.data.fields.NumericalJointObsField method) (scvi.data.fields.ObsmField method) (scvi.data.fields.ProteinObsmField method) (scvi.data.fields.StringUnsField method) register_fields() (scvi.data.AnnDataManager method) register_manager() (scvi.external.CellAssign class method) (scvi.external.GIMVI class method) (scvi.external.RNAStereoscope class method) (scvi.external.SCAR class method) (scvi.external.SOLO class method) (scvi.external.SpatialStereoscope class method) (scvi.model.AmortizedLDA class method) (scvi.model.AUTOZI class method) (scvi.model.base.BaseLatentModeModelClass class method) (scvi.model.base.BaseModelClass class method) (scvi.model.CondSCVI class method) (scvi.model.DestVI class method) (scvi.model.JaxSCVI class method) (scvi.model.LinearSCVI class method) (scvi.model.MULTIVI class method) (scvi.model.PEAKVI class method) (scvi.model.SCANVI class method) (scvi.model.SCVI class method) (scvi.model.TOTALVI class method) register_new_fields() (scvi.data.AnnDataManager method) registered_keys (scvi.dataloaders.AnnTorchDataset attribute) registry (scvi.data.AnnDataManager attribute) registry_key (scvi.data.fields.BaseAnnDataField attribute) (scvi.data.fields.BaseMuDataWrapperClass attribute) (scvi.data.fields.CategoricalJointObsField attribute) (scvi.data.fields.CategoricalObsField attribute) (scvi.data.fields.LabelsWithUnlabeledObsField attribute) (scvi.data.fields.LayerField attribute) (scvi.data.fields.MuDataCategoricalJointObsField attribute) (scvi.data.fields.MuDataCategoricalObsField attribute) (scvi.data.fields.MuDataLayerField attribute) (scvi.data.fields.MuDataNumericalJointObsField attribute) (scvi.data.fields.MuDataNumericalObsField attribute) (scvi.data.fields.MuDataObsmField attribute) (scvi.data.fields.MuDataProteinLayerField attribute) (scvi.data.fields.NumericalJointObsField attribute) (scvi.data.fields.ObsmField attribute) (scvi.data.fields.ProteinObsmField attribute) (scvi.data.fields.StringUnsField attribute) reparametrized_params (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) required_rngs (scvi.module.JaxVAE attribute) resample_labels() (scvi.dataloaders.SemiSupervisedDataLoader method) rescale_dropout() (scvi.module.AutoZIVAE method) reset_logging_handler() (scvi._settings.ScviConfig method) reshape_bernoulli() (scvi.module.AutoZIVAE method) retina() (in module scvi.data) RNADeconv (class in scvi.external.stereoscope) RNASeqMixin (class in scvi.model.base) RNAStereoscope (class in scvi.external) rngs (scvi.module.base.JaxModuleWrapper attribute) rsample() (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.ZeroInflatedNegativeBinomial method) S sample() (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.ZeroInflatedNegativeBinomial method) (scvi.external.cellassign.CellAssignModule method) (scvi.external.stereoscope.RNADeconv method) (scvi.external.stereoscope.SpatialDeconv method) (scvi.module.base.BaseModuleClass method) (scvi.module.MRDeconv method) (scvi.module.TOTALVAE method) (scvi.module.VAE method) (scvi.module.VAEC method) sample_bernoulli_params() (scvi.module.AutoZIVAE method) sample_from_beta_distribution() (scvi.module.AutoZIVAE method) sample_from_posterior_l() (scvi.external.gimvi.JVAE method) sample_from_posterior_z() (scvi.external.gimvi.JVAE method) sample_n() (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.ZeroInflatedNegativeBinomial method) sample_posterior() (scvi.model.base.PyroSampleMixin method) sample_rate() (scvi.external.gimvi.JVAE method) sample_scale() (scvi.external.gimvi.JVAE method) sample_with_intermediates() (scvi.distributions.JaxNegativeBinomialMeanDisp method) sampler (scvi.dataloaders.AnnDataLoader attribute) (scvi.dataloaders.ConcatDataLoader attribute) (scvi.dataloaders.SemiSupervisedDataLoader attribute) save() (scvi.external.CellAssign method) (scvi.external.GIMVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.model.AmortizedLDA method) (scvi.model.AUTOZI method) (scvi.model.base.BaseLatentModeModelClass method) (scvi.model.base.BaseModelClass method) (scvi.model.CondSCVI method) (scvi.model.DestVI method) (scvi.model.JaxSCVI method) (scvi.model.LinearSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) save_hyperparameters() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) SaveBestState (class in scvi.train) scale_sampler() (scvi.model.base.DifferentialComputation method) SCANVAE (class in scvi.module) SCANVI (class in scvi.model) SCAR (class in scvi.external) scope (scvi.module.JaxVAE attribute) SCVI (class in scvi.model) ScviConfig (class in scvi._settings) seed (scvi._settings.ScviConfig attribute) SemiSupervisedDataLoader (class in scvi.dataloaders) SemiSupervisedDataSplitter (class in scvi.dataloaders) SemiSupervisedTrainingPlan (class in scvi.train) seqfish() (in module scvi.data) seqfishplus() (in module scvi.data) set_default_validate_args() (scvi.distributions.JaxNegativeBinomialMeanDisp static method) (scvi.distributions.NegativeBinomial static method) (scvi.distributions.NegativeBinomialMixture static method) (scvi.distributions.ZeroInflatedNegativeBinomial static method) set_online_update_hooks() (scvi.nn.FCLayers method) set_train_state() (scvi.train.JaxTrainingPlan method) setup() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.model.base.PyroJitGuideWarmup method) (scvi.module.JaxVAE method) setup_anndata() (scvi.external.CellAssign class method) (scvi.external.GIMVI class method) (scvi.external.RNAStereoscope class method) (scvi.external.SCAR class method) (scvi.external.SOLO class method) (scvi.external.SpatialStereoscope class method) (scvi.model.AmortizedLDA class method) (scvi.model.AUTOZI class method) (scvi.model.base.BaseLatentModeModelClass class method) (scvi.model.base.BaseModelClass class method) (scvi.model.CondSCVI class method) (scvi.model.DestVI class method) (scvi.model.JaxSCVI class method) (scvi.model.LinearSCVI class method) (scvi.model.MULTIVI class method) (scvi.model.PEAKVI class method) (scvi.model.SCANVI class method) (scvi.model.SCVI class method) (scvi.model.TOTALVI class method) setup_anndata_dsp (in module scvi.utils) setup_data_attr() (scvi.dataloaders.AnnTorchDataset method) setup_getitem() (scvi.dataloaders.AnnTorchDataset method) setup_mudata() (scvi.model.TOTALVI class method) shape() (scvi.distributions.JaxNegativeBinomialMeanDisp method) smfish() (in module scvi.data) SOLO (class in scvi.external) SpatialDeconv (class in scvi.external.stereoscope) SpatialStereoscope (class in scvi.external) spleen_lymph_cite_seq() (in module scvi.data) state (scvi.module.base.JaxModuleWrapper attribute) state_dict() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.model.base.PyroJitGuideWarmup method) (scvi.module.base.JaxModuleWrapper method) state_key (scvi.model.base.PyroJitGuideWarmup attribute) stddev (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) StringUnsField (class in scvi.data.fields) subsample_labels() (scvi.dataloaders.SemiSupervisedDataLoader method) summary_stats (scvi.data.AnnDataManager attribute) support (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) T teardown() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.model.base.PyroJitGuideWarmup method) (scvi.train.LoudEarlyStopping method) test_dataloader() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) test_indices (scvi.external.CellAssign attribute) (scvi.external.GIMVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.model.AmortizedLDA attribute) (scvi.model.AUTOZI attribute) (scvi.model.base.BaseLatentModeModelClass attribute) (scvi.model.base.BaseModelClass attribute) (scvi.model.CondSCVI attribute) (scvi.model.DestVI attribute) (scvi.model.JaxSCVI attribute) (scvi.model.LinearSCVI attribute) (scvi.model.MULTIVI attribute) (scvi.model.PEAKVI attribute) (scvi.model.SCANVI attribute) (scvi.model.SCVI attribute) (scvi.model.TOTALVI attribute) timeout (scvi.dataloaders.AnnDataLoader attribute) (scvi.dataloaders.ConcatDataLoader attribute) (scvi.dataloaders.SemiSupervisedDataLoader attribute) to() (scvi.module.base.JaxModuleWrapper method) to_device() (scvi.external.CellAssign method) (scvi.external.GIMVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.model.AmortizedLDA method) (scvi.model.AUTOZI method) (scvi.model.base.BaseLatentModeModelClass method) (scvi.model.base.BaseModelClass method) (scvi.model.CondSCVI method) (scvi.model.DestVI method) (scvi.model.JaxSCVI method) (scvi.model.LinearSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) to_dict() (scvi.utils.attrdict method) to_event() (scvi.distributions.JaxNegativeBinomialMeanDisp method) to_json() (scvi.utils.attrdict method) to_json_best_effort() (scvi.utils.attrdict method) to_latent_mode() (scvi.model.base.BaseLatentModeModelClass method) (scvi.model.SCVI method) to_yaml() (scvi.utils.attrdict method) topic_by_feature() (scvi.module.AmortizedLDAPyroModule method) TOTALVAE (class in scvi.module) TOTALVI (class in scvi.model) track() (in module scvi.utils) train() (scvi.external.CellAssign method) (scvi.external.GIMVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.model.AmortizedLDA method) (scvi.model.AUTOZI method) (scvi.model.base.BaseLatentModeModelClass method) (scvi.model.base.BaseModelClass method) (scvi.model.base.PyroSviTrainMixin method) (scvi.model.base.UnsupervisedTrainingMixin method) (scvi.model.CondSCVI method) (scvi.model.DestVI method) (scvi.model.JaxSCVI method) (scvi.model.LinearSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) (scvi.module.base.JaxModuleWrapper method) train_dataloader() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) train_indices (scvi.external.CellAssign attribute) (scvi.external.GIMVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.model.AmortizedLDA attribute) (scvi.model.AUTOZI attribute) (scvi.model.base.BaseLatentModeModelClass attribute) (scvi.model.base.BaseModelClass attribute) (scvi.model.CondSCVI attribute) (scvi.model.DestVI attribute) (scvi.model.JaxSCVI attribute) (scvi.model.LinearSCVI attribute) (scvi.model.MULTIVI attribute) (scvi.model.PEAKVI attribute) (scvi.model.SCANVI attribute) (scvi.model.SCVI attribute) (scvi.model.TOTALVI attribute) train_state (scvi.module.base.JaxModuleWrapper attribute) Trainer (class in scvi.train) training (scvi.external.cellassign.CellAssignModule attribute) (scvi.external.gimvi.JVAE attribute) (scvi.external.stereoscope.RNADeconv attribute) (scvi.external.stereoscope.SpatialDeconv attribute) (scvi.module.AmortizedLDAPyroModule attribute) (scvi.module.AutoZIVAE attribute) (scvi.module.base.BaseLatentModeModuleClass attribute) (scvi.module.base.BaseModuleClass attribute) (scvi.module.base.JaxModuleWrapper attribute) (scvi.module.base.PyroBaseModuleClass attribute) (scvi.module.Classifier attribute) (scvi.module.JaxVAE attribute) (scvi.module.LDVAE attribute) (scvi.module.MRDeconv attribute) (scvi.module.MULTIVAE attribute) (scvi.module.PEAKVAE attribute) (scvi.module.SCANVAE attribute) (scvi.module.TOTALVAE attribute) (scvi.module.VAE attribute) (scvi.module.VAEC attribute) (scvi.nn.Decoder attribute) (scvi.nn.Encoder attribute) (scvi.nn.FCLayers attribute) (scvi.train.AdversarialTrainingPlan attribute) (scvi.train.JaxTrainingPlan attribute) (scvi.train.PyroTrainingPlan attribute) (scvi.train.SemiSupervisedTrainingPlan attribute) (scvi.train.TrainingPlan attribute) training_epoch_end() (scvi.train.PyroTrainingPlan method) training_step() (scvi.train.AdversarialTrainingPlan method) (scvi.train.JaxTrainingPlan method) (scvi.train.PyroTrainingPlan method) (scvi.train.SemiSupervisedTrainingPlan method) (scvi.train.TrainingPlan method) TrainingPlan (class in scvi.train) TrainRunner (class in scvi.train) transfer_batch_to_device() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.train.JaxTrainingPlan static method) transfer_field() (scvi.data.fields.BaseAnnDataField method) (scvi.data.fields.BaseMuDataWrapperClass method) (scvi.data.fields.CategoricalJointObsField method) (scvi.data.fields.CategoricalObsField method) (scvi.data.fields.LabelsWithUnlabeledObsField method) (scvi.data.fields.LayerField method) (scvi.data.fields.MuDataCategoricalJointObsField method) (scvi.data.fields.MuDataCategoricalObsField method) (scvi.data.fields.MuDataLayerField method) (scvi.data.fields.MuDataNumericalJointObsField method) (scvi.data.fields.MuDataNumericalObsField method) (scvi.data.fields.MuDataObsmField method) (scvi.data.fields.MuDataProteinLayerField method) (scvi.data.fields.NumericalJointObsField method) (scvi.data.fields.ObsmField method) (scvi.data.fields.ProteinObsmField method) (scvi.data.fields.StringUnsField method) transfer_fields() (scvi.data.AnnDataManager method) tree_flatten() (scvi.distributions.JaxNegativeBinomialMeanDisp method) tree_unflatten() (scvi.distributions.JaxNegativeBinomialMeanDisp class method) U UNLABELED_CATEGORY (scvi.data.fields.LabelsWithUnlabeledObsField attribute) unlock() (scvi.utils.attrdict method) unlocked() (scvi.utils.attrdict method) UnsupervisedTrainingMixin (class in scvi.model.base) update() (scvi.utils.attrdict method) update_from_flattened_dict() (scvi.utils.attrdict method) update_setup_method_args() (scvi.data.AnnDataManager method) V VAE (class in scvi.module) VAEC (class in scvi.module) VAEMixin (class in scvi.model.base) val_dataloader() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) validate() (scvi.data.AnnDataManager method) validate_field() (scvi.data.fields.BaseAnnDataField method) (scvi.data.fields.BaseMuDataWrapperClass method) (scvi.data.fields.CategoricalJointObsField method) (scvi.data.fields.CategoricalObsField method) (scvi.data.fields.LabelsWithUnlabeledObsField method) (scvi.data.fields.LayerField method) (scvi.data.fields.MuDataCategoricalJointObsField method) (scvi.data.fields.MuDataCategoricalObsField method) (scvi.data.fields.MuDataLayerField method) (scvi.data.fields.MuDataNumericalJointObsField method) (scvi.data.fields.MuDataNumericalObsField method) (scvi.data.fields.MuDataObsmField method) (scvi.data.fields.MuDataProteinLayerField method) (scvi.data.fields.NumericalJointObsField method) (scvi.data.fields.ObsmField method) (scvi.data.fields.ProteinObsmField method) (scvi.data.fields.StringUnsField method) validation_indices (scvi.external.CellAssign attribute) (scvi.external.GIMVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.model.AmortizedLDA attribute) (scvi.model.AUTOZI attribute) (scvi.model.base.BaseLatentModeModelClass attribute) (scvi.model.base.BaseModelClass attribute) (scvi.model.CondSCVI attribute) (scvi.model.DestVI attribute) (scvi.model.JaxSCVI attribute) (scvi.model.LinearSCVI attribute) (scvi.model.MULTIVI attribute) (scvi.model.PEAKVI attribute) (scvi.model.SCANVI attribute) (scvi.model.SCVI attribute) (scvi.model.TOTALVI attribute) validation_step() (scvi.train.JaxTrainingPlan method) (scvi.train.SemiSupervisedTrainingPlan method) (scvi.train.TrainingPlan method) values() (scvi.utils.attrdict method) variance (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) verbosity (scvi._settings.ScviConfig attribute) view_anndata_setup() (scvi.external.CellAssign method) (scvi.external.GIMVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.model.AmortizedLDA method) (scvi.model.AUTOZI method) (scvi.model.base.BaseLatentModeModelClass method) (scvi.model.base.BaseModelClass method) (scvi.model.CondSCVI method) (scvi.model.DestVI method) (scvi.model.JaxSCVI method) (scvi.model.LinearSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) view_registry() (scvi.data.AnnDataManager method) view_setup_args() (scvi.external.CellAssign static method) (scvi.external.GIMVI static method) (scvi.external.RNAStereoscope static method) (scvi.external.SCAR static method) (scvi.external.SOLO static method) (scvi.external.SpatialStereoscope static method) (scvi.model.AmortizedLDA static method) (scvi.model.AUTOZI static method) (scvi.model.base.BaseLatentModeModelClass static method) (scvi.model.base.BaseModelClass static method) (scvi.model.CondSCVI static method) (scvi.model.DestVI static method) (scvi.model.JaxSCVI static method) (scvi.model.LinearSCVI static method) (scvi.model.MULTIVI static method) (scvi.model.PEAKVI static method) (scvi.model.SCANVI static method) (scvi.model.SCVI static method) (scvi.model.TOTALVI static method) view_setup_method_args() (scvi.data.AnnDataManager static method) view_state_registry() (scvi.data.fields.BaseAnnDataField method) (scvi.data.fields.BaseMuDataWrapperClass method) (scvi.data.fields.CategoricalJointObsField method) (scvi.data.fields.CategoricalObsField method) (scvi.data.fields.LabelsWithUnlabeledObsField method) (scvi.data.fields.LayerField method) (scvi.data.fields.MuDataCategoricalJointObsField method) (scvi.data.fields.MuDataCategoricalObsField method) (scvi.data.fields.MuDataLayerField method) (scvi.data.fields.MuDataNumericalJointObsField method) (scvi.data.fields.MuDataNumericalObsField method) (scvi.data.fields.MuDataObsmField method) (scvi.data.fields.MuDataProteinLayerField method) (scvi.data.fields.NumericalJointObsField method) (scvi.data.fields.ObsmField method) (scvi.data.fields.ProteinObsmField method) (scvi.data.fields.StringUnsField method) Z ZeroInflatedNegativeBinomial (class in scvi.distributions) zi_logits (scvi.distributions.ZeroInflatedNegativeBinomial attribute) zi_probs (scvi.distributions.ZeroInflatedNegativeBinomial attribute)