Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | Z A adata (scvi.external.CellAssign attribute) (scvi.external.ContrastiveVI attribute) (scvi.external.GIMVI attribute) (scvi.external.POISSONVI 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.ContrastiveVI attribute) (scvi.external.GIMVI attribute) (scvi.external.POISSONVI 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_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.data) 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 calibration_error() (scvi.criticism.PosteriorPredictiveCheck method) 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.base.LossOutput attribute) classification_loss() (scvi.module.SCANVAE method) Classifier (class in scvi.module) classify() (scvi.module.SCANVAE method) coefficient_of_variation() (scvi.criticism.PosteriorPredictiveCheck 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.SemiSupervisedTrainingPlan method) (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) ContrastiveVAE (class in scvi.external.contrastivevi) ContrastiveVI (class in scvi.external) convert_dict (scvi.utils.attrdict attribute) convert_legacy_save() (scvi.external.CellAssign class method) (scvi.external.ContrastiveVI class method) (scvi.external.GIMVI class method) (scvi.external.POISSONVI 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) create_torch_dataset() (scvi.data.AnnDataManager method) D data (scvi.data.AnnTorchDataset attribute) 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) DEFAULT_MOTIF_DIR (scvi.external.SCBASSET attribute) deregister_manager() (scvi.external.CellAssign method) (scvi.external.ContrastiveVI method) (scvi.external.GIMVI method) (scvi.external.POISSONVI 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) description (scvi.hub.HubModelCardHelper attribute) DestVI (class in scvi.model) device (scvi.external.CellAssign attribute) (scvi.external.ContrastiveVI attribute) (scvi.external.GIMVI attribute) (scvi.external.POISSONVI 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.external.POISSONVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) differential_expression() (scvi.criticism.PosteriorPredictiveCheck method) (scvi.external.ContrastiveVI method) (scvi.external.POISSONVI method) (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) 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) filter_outlier_cells() (scvi.model.base.DifferentialComputation method) 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_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) frontalcortex_dropseq() (in module scvi.data) G gather_pytree_aux_fields() (scvi.distributions.JaxNegativeBinomialMeanDisp class method) gather_pytree_data_fields() (scvi.distributions.JaxNegativeBinomialMeanDisp class method) gene_likelihood (scvi.module.JaxVAE attribute) generative() (scvi.external.cellassign.CellAssignModule method) (scvi.external.contrastivevi.ContrastiveVAE 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.utils.attrdict method) get_accessibility_estimates() (scvi.external.POISSONVI method) (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.ContrastiveVI method) (scvi.external.GIMVI method) (scvi.external.POISSONVI 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_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.POISSONVI 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.POISSONVI method) (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.ContrastiveVI method) (scvi.external.GIMVI method) (scvi.external.POISSONVI 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_jit_inference_fn() (scvi.module.base.JaxBaseModuleClass method) get_latent_library_size() (scvi.external.ContrastiveVI method) (scvi.external.POISSONVI method) (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.ContrastiveVI method) (scvi.external.GIMVI method) (scvi.external.POISSONVI 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.external.POISSONVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) get_likelihood_parameters() (scvi.external.POISSONVI method) (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.POISSONVI 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_max_epochs_heuristic() (in module scvi.model) 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.ContrastiveVI method) (scvi.external.POISSONVI method) (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.POISSONVI 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.external.POISSONVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) get_salient_normalized_expression() (scvi.external.ContrastiveVI 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_specific_normalized_expression() (scvi.external.ContrastiveVI 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_tf_activity() (scvi.external.SCBASSET 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.ContrastiveVI attribute) (scvi.external.GIMVI attribute) (scvi.external.POISSONVI 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.contrastivevi.ContrastiveVAE 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.ContrastiveVI attribute) (scvi.external.GIMVI attribute) (scvi.external.POISSONVI 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.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.utils.attrdict method) keys_and_dtypes (scvi.data.AnnTorchDataset attribute) 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) latent_kl_divergence() (scvi.external.contrastivevi.ContrastiveVAE static method) LayerField (class in scvi.data.fields) LDVAE (class in scvi.module) library_kl_divergence() (scvi.external.contrastivevi.ContrastiveVAE method) 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.ContrastiveVI class method) (scvi.external.GIMVI class method) (scvi.external.POISSONVI 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 method) (scvi.dataloaders.SemiSupervisedDataSplitter method) load_model() (scvi.hub.HubModel method) load_query_data() (scvi.external.POISSONVI class method) (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.ContrastiveVI static method) (scvi.external.GIMVI static method) (scvi.external.POISSONVI 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) local_dir (scvi.hub.HubModel attribute) lock() (scvi.utils.attrdict method) log_prob() (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.ZeroInflatedNegativeBinomial method) log_with_mode() (scvi.train.SemiSupervisedTrainingPlan method) logging_dir (scvi._settings.ScviConfig attribute) logits (scvi.module.base.LossOutput attribute) loss (scvi.module.base.LossOutput attribute) loss() (scvi.external.cellassign.CellAssignModule method) (scvi.external.contrastivevi.ContrastiveVAE 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.HubMetadata attribute) (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) MOTIF_URLS (scvi.external.SCBASSET attribute) 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) (scvi.module.SCANVAE method) on_load_checkpoint() (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.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) (scvi.train.SaveCheckpoint 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) (scvi.train.AdversarialTrainingPlan method) (scvi.train.LowLevelPyroTrainingPlan 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_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) (scvi.train.AdversarialTrainingPlan method) (scvi.train.SaveBestState 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) 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) POISSONVI (class in scvi.external) posterior_predictive_sample() (scvi.external.POISSONVI method) (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) PosteriorPredictiveCheck (class in scvi.criticism) 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.external.POISSONVI static method) (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) process_selection() (scvi.model.base.DifferentialComputation 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) pull_from_s3() (scvi.hub.HubModel class method) purified_pbmc_dataset() (in module scvi.data) push_to_huggingface_hub() (scvi.hub.HubModel method) push_to_s3() (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) pytree_aux_fields (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) pytree_data_fields (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) 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) reads_to_fragments() (in module scvi.data) reconstruction_loss (scvi.module.base.LossOutput attribute) reconstruction_loss() (scvi.external.contrastivevi.ContrastiveVAE static method) (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.ContrastiveVI class method) (scvi.external.GIMVI class method) (scvi.external.POISSONVI 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.data.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.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.contrastivevi.ContrastiveVAE 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.ContrastiveVI method) (scvi.external.GIMVI method) (scvi.external.POISSONVI 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.hub.HubMetadata method) (scvi.hub.HubModel 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) SaveCheckpoint (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) 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.ContrastiveVI class method) (scvi.external.GIMVI class method) (scvi.external.POISSONVI 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_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) summary_string (scvi.external.CellAssign attribute) (scvi.external.ContrastiveVI attribute) (scvi.external.GIMVI attribute) (scvi.external.POISSONVI 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) support (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) synthetic_iid() (in module scvi.data) 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.ContrastiveVI attribute) (scvi.external.GIMVI attribute) (scvi.external.POISSONVI 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.ContrastiveVI method) (scvi.external.GIMVI method) (scvi.external.POISSONVI 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_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.ContrastiveVI method) (scvi.external.GIMVI method) (scvi.external.POISSONVI 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.ContrastiveVI attribute) (scvi.external.GIMVI attribute) (scvi.external.POISSONVI 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.contrastivevi.ContrastiveVAE 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_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) true_labels (scvi.module.base.LossOutput attribute) 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) use_sync_dist (scvi.train.TrainingPlan attribute) 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.ContrastiveVI attribute) (scvi.external.GIMVI attribute) (scvi.external.POISSONVI 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.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.ContrastiveVI method) (scvi.external.GIMVI method) (scvi.external.POISSONVI 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.ContrastiveVI static method) (scvi.external.GIMVI static method) (scvi.external.POISSONVI 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) W warnings_stacklevel (scvi._settings.ScviConfig attribute) Z zero_fraction() (scvi.criticism.PosteriorPredictiveCheck method) ZeroInflatedNegativeBinomial (class in scvi.distributions) zi_logits (scvi.distributions.ZeroInflatedNegativeBinomial attribute) zi_probs (scvi.distributions.ZeroInflatedNegativeBinomial attribute)