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.SCBASSET attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.Tangram attribute) (scvi.hub.HubModel attribute) (scvi.model.AmortizedLDA attribute) (scvi.model.AUTOZI attribute) (scvi.model.base.BaseMinifiedModeModelClass 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.MuDataCategoricalJointVarField attribute) (scvi.data.fields.MuDataCategoricalObsField attribute) (scvi.data.fields.MuDataCategoricalVarField attribute) (scvi.data.fields.MuDataLayerField attribute) (scvi.data.fields.MuDataNumericalJointObsField attribute) (scvi.data.fields.MuDataNumericalJointVarField attribute) (scvi.data.fields.MuDataNumericalObsField attribute) (scvi.data.fields.MuDataNumericalVarField attribute) (scvi.data.fields.MuDataObsmField attribute) (scvi.data.fields.MuDataProteinLayerField attribute) (scvi.data.fields.MuDataVarmField attribute) adata_manager (scvi.external.CellAssign attribute) (scvi.external.GIMVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SCBASSET attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.Tangram attribute) (scvi.model.AmortizedLDA attribute) (scvi.model.AUTOZI attribute) (scvi.model.base.BaseMinifiedModeModelClass 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) add_dna_sequence() (in module scvi.data) additional_metrics (scvi.autotune.TuneAnalysis attribute) AdversarialTrainingPlan (class in scvi.train) AmortizedLDA (class in scvi.model) AmortizedLDAPyroModule (class in scvi.module) anndata_version (scvi.hub.HubMetadata attribute) (scvi.hub.HubModelCardHelper attribute) AnnDataLoader (class in scvi.dataloaders) AnnDataManager (class in scvi.data) AnnDataManagerValidationCheck (class in scvi.data) AnnTorchDataset (class in scvi.dataloaders) 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_bound() (scvi.module.base.JaxBaseModuleClass method) as_configdict() (scvi.utils.attrdict method) as_numpy_array() (scvi.module.base.JaxBaseModuleClass static method) attr_key (scvi.data.fields.BaseAnnDataField attribute) (scvi.data.fields.BaseMuDataWrapperClass attribute) (scvi.data.fields.CategoricalJointObsField attribute) (scvi.data.fields.CategoricalJointVarField attribute) (scvi.data.fields.CategoricalObsField attribute) (scvi.data.fields.CategoricalVarField attribute) (scvi.data.fields.LabelsWithUnlabeledObsField attribute) (scvi.data.fields.LayerField attribute) (scvi.data.fields.MuDataCategoricalJointObsField attribute) (scvi.data.fields.MuDataCategoricalJointVarField attribute) (scvi.data.fields.MuDataCategoricalObsField attribute) (scvi.data.fields.MuDataCategoricalVarField attribute) (scvi.data.fields.MuDataLayerField attribute) (scvi.data.fields.MuDataNumericalJointObsField attribute) (scvi.data.fields.MuDataNumericalJointVarField attribute) (scvi.data.fields.MuDataNumericalObsField attribute) (scvi.data.fields.MuDataNumericalVarField attribute) (scvi.data.fields.MuDataObsmField attribute) (scvi.data.fields.MuDataProteinLayerField attribute) (scvi.data.fields.MuDataVarmField attribute) (scvi.data.fields.NumericalJointObsField attribute) (scvi.data.fields.NumericalJointVarField attribute) (scvi.data.fields.ObsmField attribute) (scvi.data.fields.ProteinObsmField attribute) (scvi.data.fields.StringUnsField attribute) (scvi.data.fields.VarmField attribute) attr_keys (scvi.data.fields.CategoricalJointObsField attribute) (scvi.data.fields.CategoricalJointVarField attribute) (scvi.data.fields.NumericalJointObsField attribute) (scvi.data.fields.NumericalJointVarField attribute) attr_name (scvi.data.fields.BaseAnnDataField attribute) (scvi.data.fields.BaseMuDataWrapperClass attribute) (scvi.data.fields.CategoricalJointObsField attribute) (scvi.data.fields.CategoricalJointVarField attribute) (scvi.data.fields.CategoricalObsField attribute) (scvi.data.fields.CategoricalVarField attribute) (scvi.data.fields.LabelsWithUnlabeledObsField attribute) (scvi.data.fields.LayerField attribute) (scvi.data.fields.MuDataCategoricalJointObsField attribute) (scvi.data.fields.MuDataCategoricalJointVarField attribute) (scvi.data.fields.MuDataCategoricalObsField attribute) (scvi.data.fields.MuDataCategoricalVarField attribute) (scvi.data.fields.MuDataLayerField attribute) (scvi.data.fields.MuDataNumericalJointObsField attribute) (scvi.data.fields.MuDataNumericalJointVarField attribute) (scvi.data.fields.MuDataNumericalObsField attribute) (scvi.data.fields.MuDataNumericalVarField attribute) (scvi.data.fields.MuDataObsmField attribute) (scvi.data.fields.MuDataProteinLayerField attribute) (scvi.data.fields.MuDataVarmField attribute) (scvi.data.fields.NumericalJointObsField attribute) (scvi.data.fields.NumericalJointVarField attribute) (scvi.data.fields.ObsmField attribute) (scvi.data.fields.ProteinObsmField attribute) (scvi.data.fields.StringUnsField attribute) (scvi.data.fields.VarmField 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) BaseMinifiedModeModelClass (class in scvi.model.base) BaseMinifiedModeModuleClass (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.CategoricalVarField attribute) (scvi.data.fields.LabelsWithUnlabeledObsField attribute) CategoricalJointObsField (class in scvi.data.fields) CategoricalJointVarField (class in scvi.data.fields) CategoricalObsField (class in scvi.data.fields) CategoricalVarField (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) cellxgene() (in module scvi.data) check_fully_paired_mudata (scvi.data.AnnDataManagerValidationCheck attribute) check_if_view (scvi.data.AnnDataManagerValidationCheck attribute) 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) (scvi.data.fields.VarmField attribute) COLUMNS_KEY (scvi.data.fields.NumericalJointObsField attribute) (scvi.data.fields.NumericalJointVarField 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() (scvi.module.base.JaxBaseModuleClass method) configure_optimizers() (scvi.train.AdversarialTrainingPlan method) (scvi.train.JaxTrainingPlan method) (scvi.train.LowLevelPyroTrainingPlan method) (scvi.train.PyroTrainingPlan method) (scvi.train.TrainingPlan method) constrained (scvi.external.tangram.TangramMapper attribute) 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.SCBASSET class method) (scvi.external.SOLO class method) (scvi.external.SpatialStereoscope class method) (scvi.external.Tangram class method) (scvi.model.AmortizedLDA class method) (scvi.model.AUTOZI class method) (scvi.model.base.BaseMinifiedModeModelClass 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_is_annotated (scvi.hub.HubModelCardHelper attribute) data_is_minified (scvi.hub.HubModelCardHelper attribute) data_modalities (scvi.hub.HubModelCardHelper attribute) 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) description (scvi.hub.HubModelCardHelper attribute) DestVI (class in scvi.model) device (scvi.external.CellAssign attribute) (scvi.external.GIMVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SCBASSET attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.Tangram attribute) (scvi.model.AmortizedLDA attribute) (scvi.model.AUTOZI attribute) (scvi.model.base.BaseMinifiedModeModelClass 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.JaxBaseModuleClass attribute) dict_sum() (scvi.module.base.LossOutput static method) 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.JaxBaseModuleClass 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) extra_metrics (scvi.module.base.LossOutput attribute) extra_metrics_keys (scvi.module.base.LossOutput attribute) F FCLayers (class in scvi.nn) FIELD_KEYS_KEY (scvi.data.fields.CategoricalJointObsField attribute) (scvi.data.fields.CategoricalJointVarField attribute) fit() (scvi.autotune.ModelTuner method) (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.LowLevelPyroTrainingPlan 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_dir() (scvi.hub.HubMetadata class method) (scvi.hub.HubModelCardHelper 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) from_tuple() (scvi.autotune.TuneAnalysis method) (scvi.module.base.LossOutput 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.scbasset.ScBassetModule method) (scvi.external.stereoscope.RNADeconv method) (scvi.external.stereoscope.SpatialDeconv method) (scvi.external.tangram.TangramMapper method) (scvi.module.AutoZIVAE method) (scvi.module.base.BaseModuleClass method) (scvi.module.base.JaxBaseModuleClass 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.autotune.TuneAnalysis method) (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.SCBASSET method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.Tangram method) (scvi.model.AmortizedLDA method) (scvi.model.AUTOZI method) (scvi.model.base.BaseMinifiedModeModelClass 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_cell_bias() (scvi.external.SCBASSET 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.CategoricalJointVarField method) (scvi.data.fields.CategoricalObsField method) (scvi.data.fields.CategoricalVarField method) (scvi.data.fields.LabelsWithUnlabeledObsField method) (scvi.data.fields.LayerField method) (scvi.data.fields.MuDataCategoricalJointObsField method) (scvi.data.fields.MuDataCategoricalJointVarField method) (scvi.data.fields.MuDataCategoricalObsField method) (scvi.data.fields.MuDataCategoricalVarField method) (scvi.data.fields.MuDataLayerField method) (scvi.data.fields.MuDataNumericalJointObsField method) (scvi.data.fields.MuDataNumericalJointVarField method) (scvi.data.fields.MuDataNumericalObsField method) (scvi.data.fields.MuDataNumericalVarField method) (scvi.data.fields.MuDataObsmField method) (scvi.data.fields.MuDataProteinLayerField method) (scvi.data.fields.MuDataVarmField method) (scvi.data.fields.NumericalJointObsField method) (scvi.data.fields.NumericalJointVarField method) (scvi.data.fields.ObsmField method) (scvi.data.fields.ProteinObsmField method) (scvi.data.fields.StringUnsField method) (scvi.data.fields.VarmField 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.CategoricalJointVarField method) (scvi.data.fields.CategoricalObsField method) (scvi.data.fields.CategoricalVarField method) (scvi.data.fields.LabelsWithUnlabeledObsField method) (scvi.data.fields.LayerField method) (scvi.data.fields.MuDataCategoricalJointObsField method) (scvi.data.fields.MuDataCategoricalJointVarField method) (scvi.data.fields.MuDataCategoricalObsField method) (scvi.data.fields.MuDataCategoricalVarField method) (scvi.data.fields.MuDataLayerField method) (scvi.data.fields.MuDataNumericalJointObsField method) (scvi.data.fields.MuDataNumericalJointVarField method) (scvi.data.fields.MuDataNumericalObsField method) (scvi.data.fields.MuDataNumericalVarField method) (scvi.data.fields.MuDataObsmField method) (scvi.data.fields.MuDataProteinLayerField method) (scvi.data.fields.MuDataVarmField method) (scvi.data.fields.NumericalJointObsField method) (scvi.data.fields.NumericalJointVarField method) (scvi.data.fields.ObsmField method) (scvi.data.fields.ProteinObsmField method) (scvi.data.fields.StringUnsField method) (scvi.data.fields.VarmField 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.SCBASSET method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.Tangram method) (scvi.model.AmortizedLDA method) (scvi.model.AUTOZI method) (scvi.model.base.BaseMinifiedModeModelClass 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_init_arguments_and_types() (scvi.dataloaders.DataSplitter class method) (scvi.dataloaders.SemiSupervisedDataSplitter class method) get_jit_inference_fn() (scvi.module.base.JaxBaseModuleClass 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.external.SCBASSET 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_mapper_matrix() (scvi.external.Tangram 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_minified_adata_scrna() (in module scvi.model.utils) get_modality() (scvi.data.fields.BaseMuDataWrapperClass method) (scvi.data.fields.MuDataCategoricalJointObsField method) (scvi.data.fields.MuDataCategoricalJointVarField method) (scvi.data.fields.MuDataCategoricalObsField method) (scvi.data.fields.MuDataCategoricalVarField method) (scvi.data.fields.MuDataLayerField method) (scvi.data.fields.MuDataNumericalJointObsField method) (scvi.data.fields.MuDataNumericalJointVarField method) (scvi.data.fields.MuDataNumericalObsField method) (scvi.data.fields.MuDataNumericalVarField method) (scvi.data.fields.MuDataObsmField method) (scvi.data.fields.MuDataProteinLayerField method) (scvi.data.fields.MuDataVarmField 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_optimizer_creator() (scvi.train.JaxTrainingPlan method) (scvi.train.TrainingPlan 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.CategoricalJointVarField method) (scvi.data.fields.CategoricalObsField method) (scvi.data.fields.CategoricalVarField method) (scvi.data.fields.LabelsWithUnlabeledObsField method) (scvi.data.fields.LayerField method) (scvi.data.fields.MuDataCategoricalJointObsField method) (scvi.data.fields.MuDataCategoricalJointVarField method) (scvi.data.fields.MuDataCategoricalObsField method) (scvi.data.fields.MuDataCategoricalVarField method) (scvi.data.fields.MuDataLayerField method) (scvi.data.fields.MuDataNumericalJointObsField method) (scvi.data.fields.MuDataNumericalJointVarField method) (scvi.data.fields.MuDataNumericalObsField method) (scvi.data.fields.MuDataNumericalVarField method) (scvi.data.fields.MuDataObsmField method) (scvi.data.fields.MuDataProteinLayerField method) (scvi.data.fields.MuDataVarmField method) (scvi.data.fields.NumericalJointObsField method) (scvi.data.fields.NumericalJointVarField method) (scvi.data.fields.ObsmField method) (scvi.data.fields.ProteinObsmField method) (scvi.data.fields.StringUnsField method) (scvi.data.fields.VarmField 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.SCBASSET attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.Tangram attribute) (scvi.model.AmortizedLDA attribute) (scvi.model.AUTOZI attribute) (scvi.model.base.BaseMinifiedModeModelClass 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) HubMetadata (class in scvi.hub) HubModel (class in scvi.hub) HubModelCardHelper (class in scvi.hub) 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.scbasset.ScBassetModule method) (scvi.external.stereoscope.RNADeconv method) (scvi.external.stereoscope.SpatialDeconv method) (scvi.external.tangram.TangramMapper method) (scvi.module.base.BaseMinifiedModeModuleClass method) (scvi.module.base.BaseModuleClass method) (scvi.module.base.JaxBaseModuleClass 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) info() (scvi.autotune.ModelTuner method) 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.CategoricalJointVarField attribute) (scvi.data.fields.CategoricalObsField attribute) (scvi.data.fields.CategoricalVarField attribute) (scvi.data.fields.LabelsWithUnlabeledObsField attribute) (scvi.data.fields.LayerField attribute) (scvi.data.fields.MuDataCategoricalJointObsField attribute) (scvi.data.fields.MuDataCategoricalJointVarField attribute) (scvi.data.fields.MuDataCategoricalObsField attribute) (scvi.data.fields.MuDataCategoricalVarField attribute) (scvi.data.fields.MuDataLayerField attribute) (scvi.data.fields.MuDataNumericalJointObsField attribute) (scvi.data.fields.MuDataNumericalJointVarField attribute) (scvi.data.fields.MuDataNumericalObsField attribute) (scvi.data.fields.MuDataNumericalVarField attribute) (scvi.data.fields.MuDataObsmField attribute) (scvi.data.fields.MuDataProteinLayerField attribute) (scvi.data.fields.MuDataVarmField attribute) (scvi.data.fields.NumericalJointObsField attribute) (scvi.data.fields.NumericalJointVarField attribute) (scvi.data.fields.ObsmField attribute) (scvi.data.fields.ProteinObsmField attribute) (scvi.data.fields.StringUnsField attribute) (scvi.data.fields.VarmField 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.SCBASSET attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.Tangram attribute) (scvi.model.AmortizedLDA attribute) (scvi.model.AUTOZI attribute) (scvi.model.base.BaseMinifiedModeModelClass 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.autotune.TuneAnalysis method) (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) JaxBaseModuleClass (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.autotune.TuneAnalysis method) (scvi.utils.attrdict method) kl_global (scvi.module.base.LossOutput attribute) kl_global_sum (scvi.module.base.LossOutput attribute) kl_local (scvi.module.base.LossOutput attribute) kl_local_sum (scvi.module.base.LossOutput attribute) kl_weight (scvi.train.LowLevelPyroTrainingPlan attribute) (scvi.train.TrainingPlan attribute) L LabelsWithUnlabeledObsField (class in scvi.data.fields) lambda_count (scvi.external.tangram.TangramMapper attribute) lambda_d (scvi.external.tangram.TangramMapper attribute) lambda_f_reg (scvi.external.tangram.TangramMapper attribute) lambda_g1 (scvi.external.tangram.TangramMapper attribute) lambda_g2 (scvi.external.tangram.TangramMapper attribute) lambda_r (scvi.external.tangram.TangramMapper attribute) large_training_adata (scvi.hub.HubModel attribute) LayerField (class in scvi.data.fields) LDVAE (class in scvi.module) license_info (scvi.hub.HubModelCardHelper attribute) 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.SCBASSET class method) (scvi.external.SOLO class method) (scvi.external.SpatialStereoscope class method) (scvi.external.Tangram class method) (scvi.model.AmortizedLDA class method) (scvi.model.AUTOZI class method) (scvi.model.base.BaseMinifiedModeModelClass 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_model() (scvi.hub.HubModel 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.SCBASSET static method) (scvi.external.SOLO static method) (scvi.external.SpatialStereoscope static method) (scvi.external.Tangram static method) (scvi.model.AmortizedLDA static method) (scvi.model.AUTOZI static method) (scvi.model.base.BaseMinifiedModeModelClass 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.model.base.PyroModelGuideWarmup method) (scvi.module.base.JaxBaseModuleClass 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.LossOutput attribute) loss() (scvi.external.cellassign.CellAssignModule method) (scvi.external.gimvi.JVAE method) (scvi.external.scbasset.ScBassetModule method) (scvi.external.stereoscope.RNADeconv method) (scvi.external.stereoscope.SpatialDeconv method) (scvi.external.tangram.TangramMapper method) (scvi.module.AutoZIVAE method) (scvi.module.base.BaseModuleClass method) (scvi.module.base.JaxBaseModuleClass 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) LossOutput (class in scvi.module.base) LoudEarlyStopping (class in scvi.train) LowLevelPyroTrainingPlan (class in scvi.train) M MAPPINGS_KEY (scvi.data.fields.CategoricalJointObsField attribute) (scvi.data.fields.CategoricalJointVarField 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) metadata (scvi.hub.HubModel attribute) metric (scvi.autotune.TuneAnalysis attribute) minified_data_type (scvi.model.base.BaseMinifiedModeModelClass attribute) (scvi.model.SCANVI attribute) (scvi.model.SCVI attribute) (scvi.module.base.BaseMinifiedModeModuleClass attribute) minify_adata() (scvi.model.base.BaseMinifiedModeModelClass method) (scvi.model.SCANVI method) (scvi.model.SCVI method) 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.CategoricalJointVarField attribute) (scvi.data.fields.CategoricalObsField attribute) (scvi.data.fields.CategoricalVarField attribute) (scvi.data.fields.LabelsWithUnlabeledObsField attribute) (scvi.data.fields.LayerField attribute) (scvi.data.fields.MuDataCategoricalJointObsField attribute) (scvi.data.fields.MuDataCategoricalJointVarField attribute) (scvi.data.fields.MuDataCategoricalObsField attribute) (scvi.data.fields.MuDataCategoricalVarField attribute) (scvi.data.fields.MuDataLayerField attribute) (scvi.data.fields.MuDataNumericalJointObsField attribute) (scvi.data.fields.MuDataNumericalJointVarField attribute) (scvi.data.fields.MuDataNumericalObsField attribute) (scvi.data.fields.MuDataNumericalVarField attribute) (scvi.data.fields.MuDataObsmField attribute) (scvi.data.fields.MuDataProteinLayerField attribute) (scvi.data.fields.MuDataVarmField attribute) (scvi.data.fields.NumericalJointObsField attribute) (scvi.data.fields.NumericalJointVarField attribute) (scvi.data.fields.ObsmField attribute) (scvi.data.fields.ProteinObsmField attribute) (scvi.data.fields.StringUnsField attribute) (scvi.data.fields.VarmField attribute) mode (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) model (scvi.hub.HubModel attribute) (scvi.module.AmortizedLDAPyroModule attribute) (scvi.module.base.PyroBaseModuleClass attribute) model_card (scvi.hub.HubModel attribute) model_cls_name (scvi.hub.HubModelCardHelper attribute) model_data_registry (scvi.hub.HubModelCardHelper attribute) model_init_params (scvi.hub.HubModelCardHelper attribute) model_kwargs (scvi.autotune.TuneAnalysis attribute) model_parent_module (scvi.hub.HubMetadata attribute) (scvi.hub.HubModelCardHelper attribute) model_setup_anndata_args (scvi.hub.HubModelCardHelper attribute) model_summary_stats (scvi.hub.HubModelCardHelper attribute) ModelTuner (class in scvi.autotune) mouse_ob_dataset() (in module scvi.data) MRDeconv (class in scvi.module) MuDataCategoricalJointObsField (class in scvi.data.fields) MuDataCategoricalJointVarField (class in scvi.data.fields) MuDataCategoricalObsField (class in scvi.data.fields) MuDataCategoricalVarField (class in scvi.data.fields) MuDataLayerField (class in scvi.data.fields) MuDataNumericalJointObsField (class in scvi.data.fields) MuDataNumericalJointVarField (class in scvi.data.fields) MuDataNumericalObsField (class in scvi.data.fields) MuDataNumericalVarField (class in scvi.data.fields) MuDataObsmField (class in scvi.data.fields) MuDataProteinLayerField (class in scvi.data.fields) MuDataVarmField (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) (scvi.data.fields.CategoricalJointVarField 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_minibatch (scvi.module.base.LossOutput attribute) n_obs_sc (scvi.external.tangram.TangramMapper attribute) n_obs_sp (scvi.external.tangram.TangramMapper attribute) n_obs_training (scvi.train.LowLevelPyroTrainingPlan 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.external.tangram.TangramMapper attribute) (scvi.module.base.JaxBaseModuleClass 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) NumericalJointVarField (class in scvi.data.fields) O ObsmField (class in scvi.data.fields) on_after_backward() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_after_batch_transfer() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) on_before_backward() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_before_batch_transfer() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) on_before_optimizer_step() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_before_zero_grad() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_exception() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_fit_end() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_fit_start() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_load() (scvi.module.base.BaseModuleClass method) (scvi.module.base.JaxBaseModuleClass static method) (scvi.module.base.PyroBaseModuleClass method) on_load_checkpoint() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_predict_batch_end() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_predict_batch_start() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_predict_end() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_predict_epoch_end() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_predict_epoch_start() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_predict_start() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_sanity_check_end() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_sanity_check_start() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_save_checkpoint() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_test_batch_end() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_test_batch_start() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_test_end() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_test_epoch_end() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_test_epoch_start() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_test_start() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_train_batch_end() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_train_batch_start() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_train_end() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) (scvi.train.SaveBestState method) on_train_epoch_end() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_train_epoch_start() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_train_start() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) (scvi.train.SaveBestState method) on_val_epoch_end() (scvi.train.SaveBestState method) on_validation_batch_end() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_validation_batch_start() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_validation_end() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_validation_epoch_end() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_validation_epoch_start() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_validation_start() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup 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.CategoricalVarField attribute) (scvi.data.fields.LabelsWithUnlabeledObsField attribute) P params (scvi.module.base.JaxBaseModuleClass attribute) parent (scvi.external.tangram.TangramMapper attribute) (scvi.module.base.JaxBaseModuleClass attribute) (scvi.module.JaxVAE attribute) parse_argparser() (scvi.dataloaders.DataSplitter class method) (scvi.dataloaders.SemiSupervisedDataSplitter class method) 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.MuDataCategoricalJointVarField method) (scvi.data.fields.MuDataCategoricalObsField method) (scvi.data.fields.MuDataCategoricalVarField method) (scvi.data.fields.MuDataLayerField method) (scvi.data.fields.MuDataNumericalJointObsField method) (scvi.data.fields.MuDataNumericalJointVarField method) (scvi.data.fields.MuDataNumericalObsField method) (scvi.data.fields.MuDataNumericalVarField method) (scvi.data.fields.MuDataObsmField method) (scvi.data.fields.MuDataProteinLayerField method) (scvi.data.fields.MuDataVarmField method) progress_bar_style (scvi._settings.ScviConfig attribute) project_cell_annotations() (scvi.external.Tangram static method) project_genes() (scvi.external.Tangram static method) PROTEIN_BATCH_MASK (scvi.data.fields.ProteinObsmField attribute) ProteinObsmField (class in scvi.data.fields) pull_from_huggingface_hub() (scvi.hub.HubModel class method) purified_pbmc_dataset() (in module scvi.data) push_to_huggingface_hub() (scvi.hub.HubModel method) PyroBaseModuleClass (class in scvi.module.base) PyroJitGuideWarmup (class in scvi.model.base) PyroModelGuideWarmup (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_adata() (scvi.hub.HubModel method) read_csv() (in module scvi.data) read_h5ad() (in module scvi.data) read_large_training_adata() (scvi.hub.HubModel method) read_loom() (in module scvi.data) read_text() (in module scvi.data) reconstruction_loss (scvi.module.base.LossOutput attribute) reconstruction_loss() (scvi.external.gimvi.JVAE method) reconstruction_loss_sum (scvi.module.base.LossOutput attribute) references (scvi.hub.HubModelCardHelper attribute) register_field() (scvi.data.fields.BaseAnnDataField method) (scvi.data.fields.BaseMuDataWrapperClass method) (scvi.data.fields.CategoricalJointObsField method) (scvi.data.fields.CategoricalJointVarField method) (scvi.data.fields.CategoricalObsField method) (scvi.data.fields.CategoricalVarField method) (scvi.data.fields.LabelsWithUnlabeledObsField method) (scvi.data.fields.LayerField method) (scvi.data.fields.MuDataCategoricalJointObsField method) (scvi.data.fields.MuDataCategoricalJointVarField method) (scvi.data.fields.MuDataCategoricalObsField method) (scvi.data.fields.MuDataCategoricalVarField method) (scvi.data.fields.MuDataLayerField method) (scvi.data.fields.MuDataNumericalJointObsField method) (scvi.data.fields.MuDataNumericalJointVarField method) (scvi.data.fields.MuDataNumericalObsField method) (scvi.data.fields.MuDataNumericalVarField method) (scvi.data.fields.MuDataObsmField method) (scvi.data.fields.MuDataProteinLayerField method) (scvi.data.fields.MuDataVarmField method) (scvi.data.fields.NumericalJointObsField method) (scvi.data.fields.NumericalJointVarField method) (scvi.data.fields.ObsmField method) (scvi.data.fields.ProteinObsmField method) (scvi.data.fields.StringUnsField method) (scvi.data.fields.VarmField 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.SCBASSET class method) (scvi.external.SOLO class method) (scvi.external.SpatialStereoscope class method) (scvi.external.Tangram class method) (scvi.model.AmortizedLDA class method) (scvi.model.AUTOZI class method) (scvi.model.base.BaseMinifiedModeModelClass 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.CategoricalJointVarField attribute) (scvi.data.fields.CategoricalObsField attribute) (scvi.data.fields.CategoricalVarField attribute) (scvi.data.fields.LabelsWithUnlabeledObsField attribute) (scvi.data.fields.LayerField attribute) (scvi.data.fields.MuDataCategoricalJointObsField attribute) (scvi.data.fields.MuDataCategoricalJointVarField attribute) (scvi.data.fields.MuDataCategoricalObsField attribute) (scvi.data.fields.MuDataCategoricalVarField attribute) (scvi.data.fields.MuDataLayerField attribute) (scvi.data.fields.MuDataNumericalJointObsField attribute) (scvi.data.fields.MuDataNumericalJointVarField attribute) (scvi.data.fields.MuDataNumericalObsField attribute) (scvi.data.fields.MuDataNumericalVarField attribute) (scvi.data.fields.MuDataObsmField attribute) (scvi.data.fields.MuDataProteinLayerField attribute) (scvi.data.fields.MuDataVarmField attribute) (scvi.data.fields.NumericalJointObsField attribute) (scvi.data.fields.NumericalJointVarField attribute) (scvi.data.fields.ObsmField attribute) (scvi.data.fields.ProteinObsmField attribute) (scvi.data.fields.StringUnsField attribute) (scvi.data.fields.VarmField attribute) reparametrized_params (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) replace() (scvi.autotune.TuneAnalysis method) (scvi.module.base.LossOutput method) required_rngs (scvi.external.tangram.TangramMapper attribute) (scvi.module.base.JaxBaseModuleClass attribute) (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) results (scvi.autotune.TuneAnalysis attribute) 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.JaxBaseModuleClass 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.SCBASSET method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.Tangram method) (scvi.model.AmortizedLDA method) (scvi.model.AUTOZI method) (scvi.model.base.BaseMinifiedModeModelClass 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) SCBASSET (class in scvi.external) ScBassetModule (class in scvi.external.scbasset) scope (scvi.external.tangram.TangramMapper attribute) (scvi.module.base.JaxBaseModuleClass attribute) (scvi.module.JaxVAE attribute) SCVI (class in scvi.model) scvi_version (scvi.hub.HubMetadata attribute) (scvi.hub.HubModelCardHelper attribute) ScviConfig (class in scvi._settings) search_space (scvi.autotune.TuneAnalysis attribute) 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.external.tangram.TangramMapper method) (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) (scvi.module.base.JaxBaseModuleClass 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.SCBASSET class method) (scvi.external.SOLO class method) (scvi.external.SpatialStereoscope class method) (scvi.external.Tangram class method) (scvi.model.AmortizedLDA class method) (scvi.model.AUTOZI class method) (scvi.model.base.BaseMinifiedModeModelClass 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.external.Tangram class method) (scvi.model.TOTALVI class method) shape() (scvi.distributions.JaxNegativeBinomialMeanDisp method) smfish() (in module scvi.data) SOLO (class in scvi.external) source_attr_name (scvi.data.fields.CategoricalJointObsField attribute) (scvi.data.fields.CategoricalJointVarField attribute) (scvi.data.fields.NumericalJointObsField attribute) (scvi.data.fields.NumericalJointVarField attribute) SpatialDeconv (class in scvi.external.stereoscope) SpatialStereoscope (class in scvi.external) spleen_lymph_cite_seq() (in module scvi.data) state (scvi.module.base.JaxBaseModuleClass attribute) state_dict() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) (scvi.module.base.JaxBaseModuleClass method) state_key (scvi.model.base.PyroJitGuideWarmup attribute) (scvi.model.base.PyroModelGuideWarmup 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 Tangram (class in scvi.external) TangramMapper (class in scvi.external.tangram) target_count (scvi.external.tangram.TangramMapper attribute) teardown() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup 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.SCBASSET attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.Tangram attribute) (scvi.model.AmortizedLDA attribute) (scvi.model.AUTOZI attribute) (scvi.model.base.BaseMinifiedModeModelClass 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) tissues (scvi.hub.HubModelCardHelper attribute) to() (scvi.module.base.JaxBaseModuleClass method) to_device() (scvi.external.CellAssign method) (scvi.external.GIMVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SCBASSET method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.Tangram method) (scvi.model.AmortizedLDA method) (scvi.model.AUTOZI method) (scvi.model.base.BaseMinifiedModeModelClass 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_tuple() (scvi.autotune.TuneAnalysis method) (scvi.module.base.LossOutput 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.SCBASSET method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.Tangram method) (scvi.model.AmortizedLDA method) (scvi.model.AUTOZI method) (scvi.model.base.BaseMinifiedModeModelClass 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.JaxBaseModuleClass 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.SCBASSET attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.Tangram attribute) (scvi.model.AmortizedLDA attribute) (scvi.model.AUTOZI attribute) (scvi.model.base.BaseMinifiedModeModelClass 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_kwargs (scvi.autotune.TuneAnalysis attribute) Trainer (class in scvi.train) training (scvi.external.cellassign.CellAssignModule attribute) (scvi.external.gimvi.JVAE attribute) (scvi.external.scbasset.ScBassetModule attribute) (scvi.external.stereoscope.RNADeconv attribute) (scvi.external.stereoscope.SpatialDeconv attribute) (scvi.external.tangram.TangramMapper attribute) (scvi.module.AmortizedLDAPyroModule attribute) (scvi.module.AutoZIVAE attribute) (scvi.module.base.BaseMinifiedModeModuleClass attribute) (scvi.module.base.BaseModuleClass 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.LowLevelPyroTrainingPlan attribute) (scvi.train.PyroTrainingPlan attribute) (scvi.train.SemiSupervisedTrainingPlan attribute) (scvi.train.TrainingPlan attribute) training_code_url (scvi.hub.HubModelCardHelper attribute) training_data_url (scvi.hub.HubMetadata attribute) (scvi.hub.HubModelCardHelper attribute) training_epoch_end() (scvi.train.LowLevelPyroTrainingPlan method) training_step() (scvi.train.AdversarialTrainingPlan method) (scvi.train.JaxTrainingPlan method) (scvi.train.LowLevelPyroTrainingPlan 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.CategoricalJointVarField method) (scvi.data.fields.CategoricalObsField method) (scvi.data.fields.CategoricalVarField method) (scvi.data.fields.LabelsWithUnlabeledObsField method) (scvi.data.fields.LayerField method) (scvi.data.fields.MuDataCategoricalJointObsField method) (scvi.data.fields.MuDataCategoricalJointVarField method) (scvi.data.fields.MuDataCategoricalObsField method) (scvi.data.fields.MuDataCategoricalVarField method) (scvi.data.fields.MuDataLayerField method) (scvi.data.fields.MuDataNumericalJointObsField method) (scvi.data.fields.MuDataNumericalJointVarField method) (scvi.data.fields.MuDataNumericalObsField method) (scvi.data.fields.MuDataNumericalVarField method) (scvi.data.fields.MuDataObsmField method) (scvi.data.fields.MuDataProteinLayerField method) (scvi.data.fields.MuDataVarmField method) (scvi.data.fields.NumericalJointObsField method) (scvi.data.fields.NumericalJointVarField method) (scvi.data.fields.ObsmField method) (scvi.data.fields.ProteinObsmField method) (scvi.data.fields.StringUnsField method) (scvi.data.fields.VarmField method) transfer_fields() (scvi.data.AnnDataManager method) tree_flatten() (scvi.distributions.JaxNegativeBinomialMeanDisp method) tree_unflatten() (scvi.distributions.JaxNegativeBinomialMeanDisp class method) Tunable (class in scvi.autotune) TunableMixin (class in scvi.autotune) TuneAnalysis (class in scvi.autotune) TunerManager (class in scvi.autotune) 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.CategoricalJointVarField method) (scvi.data.fields.CategoricalObsField method) (scvi.data.fields.CategoricalVarField method) (scvi.data.fields.LabelsWithUnlabeledObsField method) (scvi.data.fields.LayerField method) (scvi.data.fields.MuDataCategoricalJointObsField method) (scvi.data.fields.MuDataCategoricalJointVarField method) (scvi.data.fields.MuDataCategoricalObsField method) (scvi.data.fields.MuDataCategoricalVarField method) (scvi.data.fields.MuDataLayerField method) (scvi.data.fields.MuDataNumericalJointObsField method) (scvi.data.fields.MuDataNumericalJointVarField method) (scvi.data.fields.MuDataNumericalObsField method) (scvi.data.fields.MuDataNumericalVarField method) (scvi.data.fields.MuDataObsmField method) (scvi.data.fields.MuDataProteinLayerField method) (scvi.data.fields.MuDataVarmField method) (scvi.data.fields.NumericalJointObsField method) (scvi.data.fields.NumericalJointVarField method) (scvi.data.fields.ObsmField method) (scvi.data.fields.ProteinObsmField method) (scvi.data.fields.StringUnsField method) (scvi.data.fields.VarmField method) validation_indices (scvi.external.CellAssign attribute) (scvi.external.GIMVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SCBASSET attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.Tangram attribute) (scvi.model.AmortizedLDA attribute) (scvi.model.AUTOZI attribute) (scvi.model.base.BaseMinifiedModeModelClass 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.autotune.TuneAnalysis method) (scvi.utils.attrdict method) variance (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) VarmField (class in scvi.data.fields) 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.SCBASSET method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.Tangram method) (scvi.model.AmortizedLDA method) (scvi.model.AUTOZI method) (scvi.model.base.BaseMinifiedModeModelClass 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.SCBASSET static method) (scvi.external.SOLO static method) (scvi.external.SpatialStereoscope static method) (scvi.external.Tangram static method) (scvi.model.AmortizedLDA static method) (scvi.model.AUTOZI static method) (scvi.model.base.BaseMinifiedModeModelClass 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.CategoricalJointVarField method) (scvi.data.fields.CategoricalObsField method) (scvi.data.fields.CategoricalVarField method) (scvi.data.fields.LabelsWithUnlabeledObsField method) (scvi.data.fields.LayerField method) (scvi.data.fields.MuDataCategoricalJointObsField method) (scvi.data.fields.MuDataCategoricalJointVarField method) (scvi.data.fields.MuDataCategoricalObsField method) (scvi.data.fields.MuDataCategoricalVarField method) (scvi.data.fields.MuDataLayerField method) (scvi.data.fields.MuDataNumericalJointObsField method) (scvi.data.fields.MuDataNumericalJointVarField method) (scvi.data.fields.MuDataNumericalObsField method) (scvi.data.fields.MuDataNumericalVarField method) (scvi.data.fields.MuDataObsmField method) (scvi.data.fields.MuDataProteinLayerField method) (scvi.data.fields.MuDataVarmField method) (scvi.data.fields.NumericalJointObsField method) (scvi.data.fields.NumericalJointVarField method) (scvi.data.fields.ObsmField method) (scvi.data.fields.ProteinObsmField method) (scvi.data.fields.StringUnsField method) (scvi.data.fields.VarmField method) Z ZeroInflatedNegativeBinomial (class in scvi.distributions) zi_logits (scvi.distributions.ZeroInflatedNegativeBinomial attribute) zi_probs (scvi.distributions.ZeroInflatedNegativeBinomial attribute)