Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | Z A adata (scvi.external.CellAssign attribute) (scvi.external.ContrastiveVI attribute) (scvi.external.Decipher attribute) (scvi.external.GIMVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI 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.external.VELOVI 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.Decipher attribute) (scvi.external.GIMVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI 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.external.VELOVI 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) add_embedding() (scvi.module.base.EmbeddingModuleMixin method) 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) approx_log_prob_tol (scvi.distributions.BetaBinomial attribute) ArchesMixin (class in scvi.model.base) arg_constraints (scvi.distributions.BetaBinomial attribute) (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.Poisson 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) AutotuneExperiment (class in scvi.autotune) 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.BetaBinomial attribute) (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.Poisson attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) batch_size (scvi._settings.ScviConfig attribute) (scvi.dataloaders.AnnDataLoader attribute) (scvi.dataloaders.ConcatDataLoader attribute) (scvi.dataloaders.SemiSupervisedDataLoader attribute) BetaBinomial (class in scvi.distributions) 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.BetaBinomial method) (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Poisson 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_decipher_time() (scvi.external.Decipher static method) compute_embedding() (scvi.module.base.EmbeddingModuleMixin method) compute_gene_patterns() (scvi.external.Decipher method) compute_global_kl_divergence() (scvi.module.AutoZIVAE method) compute_h_from_x_eps() (scvi.external.mrvi.MRVAE method) compute_imputed_gene_expression() (scvi.external.Decipher method) compute_local_statistics() (scvi.external.MRVI method) ConcatDataLoader (class in scvi.dataloaders) concentration0 (scvi.distributions.BetaBinomial attribute) concentration1 (scvi.distributions.BetaBinomial attribute) 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) conjugate_update() (scvi.distributions.BetaBinomial 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.Decipher class method) (scvi.external.GIMVI class method) (scvi.external.METHYLVI class method) (scvi.external.MRVI 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.external.VELOVI 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.autotune.AutotuneExperiment attribute) (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) Decipher (class in scvi.external) DecipherPyroModule (class in scvi.external.decipher) Decoder (class in scvi.nn) DecoderSCVI (class in scvi.nn) DEFAULT_MOTIF_DIR (scvi.external.SCBASSET attribute) deregister_manager() (scvi.external.CellAssign method) (scvi.external.ContrastiveVI method) (scvi.external.Decipher method) (scvi.external.GIMVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI 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.external.VELOVI 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.Decipher attribute) (scvi.external.decipher.DecipherPyroModule attribute) (scvi.external.GIMVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI 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.external.VELOVI 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_abundance() (scvi.external.MRVI 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.MRVI 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) differential_methylation() (scvi.external.METHYLVI method) DifferentialComputation (class in scvi.model.base) dl_num_workers (scvi._settings.ScviConfig attribute) dl_persistent_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 Embedding (class in scvi.nn) embedding_dim (scvi.nn.Embedding attribute) EmbeddingMixin (class in scvi.model.base) EmbeddingModuleMixin (class in scvi.module.base) embeddings_dict (scvi.module.base.EmbeddingModuleMixin attribute) Encoder (class in scvi.nn) encoder_n_hidden (scvi.external.mrvi.MRVAE attribute) encoder_n_layers (scvi.external.mrvi.MRVAE attribute) entropy() (scvi.distributions.BetaBinomial method) (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Poisson method) (scvi.distributions.ZeroInflatedNegativeBinomial method) enumerate_support() (scvi.distributions.BetaBinomial method) (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Poisson 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.BetaBinomial attribute) (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) event_shape (scvi.distributions.BetaBinomial attribute) (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.Poisson attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) expand() (scvi.distributions.BetaBinomial method) (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Poisson method) (scvi.distributions.ZeroInflatedNegativeBinomial method) expand_by() (scvi.distributions.BetaBinomial method) (scvi.distributions.JaxNegativeBinomialMeanDisp method) extend() (scvi.nn.Embedding class 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.train.Trainer method) forward() (scvi.module.base.BaseModuleClass method) (scvi.module.base.PyroBaseModuleClass method) (scvi.module.Classifier method) (scvi.nn.Decoder method) (scvi.nn.DecoderSCVI method) (scvi.nn.Encoder method) (scvi.nn.FCLayers method) (scvi.train.JaxTrainingPlan method) (scvi.train.LowLevelPyroTrainingPlan method) (scvi.train.TrainingPlan method) freeze (scvi.nn.Embedding attribute) 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.methylvi.METHYLVAE method) (scvi.external.mrvi.MRVAE method) (scvi.external.scbasset.ScBassetModule method) (scvi.external.stereoscope.RNADeconv method) (scvi.external.stereoscope.SpatialDeconv method) (scvi.external.tangram.TangramMapper method) (scvi.external.velovi.VELOVAE 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_aggregated_posterior() (scvi.external.MRVI 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.Decipher method) (scvi.external.GIMVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI 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.external.VELOVI 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_args() (scvi.distributions.JaxNegativeBinomialMeanDisp method) get_batch_representation() (scvi.model.base.EmbeddingMixin method) (scvi.model.SCVI 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_directional_uncertainty() (scvi.external.VELOVI method) get_elbo() (scvi.external.GIMVI method) (scvi.external.METHYLVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.VELOVI 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_embedding() (scvi.module.base.EmbeddingModuleMixin method) get_expression_fit() (scvi.external.VELOVI 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.Decipher method) (scvi.external.GIMVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI 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.external.VELOVI 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_gene_likelihood() (scvi.external.VELOVI 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.Decipher method) (scvi.external.GIMVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.SCBASSET method) (scvi.external.VELOVI 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_latent_time() (scvi.external.VELOVI 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.external.velovi.VELOVAE method) (scvi.model.LinearSCVI method) (scvi.module.LDVAE method) get_local_sample_distances() (scvi.external.MRVI method) get_local_sample_representation() (scvi.external.MRVI method) get_logger() (scvi.autotune.AutotuneExperiment method) get_mapper_matrix() (scvi.external.Tangram method) get_marginal_ll() (scvi.external.GIMVI method) (scvi.external.METHYLVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.VELOVI 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() (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Poisson method) (scvi.distributions.ZeroInflatedNegativeBinomial 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_normalized_methylation() (scvi.external.METHYLVI method) get_oneway_ref() (scvi.utils.attrdict method) get_optimizer_creator() (scvi.train.JaxTrainingPlan method) (scvi.train.TrainingPlan method) get_outlier_cell_sample_pairs() (scvi.external.MRVI method) get_params() (scvi.external.stereoscope.RNADeconv method) get_permutation_scores() (scvi.external.VELOVI 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_px() (scvi.external.velovi.VELOVAE method) get_rates() (scvi.external.VELOVI method) get_reconstruction_error() (scvi.external.GIMVI method) (scvi.external.METHYLVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.VELOVI 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_specific_normalized_methylation() (scvi.external.METHYLVI method) get_state_assignment() (scvi.external.VELOVI 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_tuner() (scvi.autotune.AutotuneExperiment method) get_type() (scvi.utils.attrdict method) get_vamp_prior() (scvi.model.CondSCVI method) get_velocity() (scvi.external.VELOVI method) GIMVI (class in scvi.external) guide (scvi.module.AmortizedLDAPyroModule attribute) (scvi.module.base.PyroBaseModuleClass attribute) guide() (scvi.external.decipher.DecipherPyroModule method) H has_enumerate_support (scvi.distributions.BetaBinomial attribute) (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.Poisson attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) has_rsample (scvi.distributions.BetaBinomial attribute) (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.Poisson attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) has_rsample_() (scvi.distributions.BetaBinomial method) heart_cell_atlas_subsampled() (in module scvi.data) history (scvi.external.CellAssign attribute) (scvi.external.ContrastiveVI attribute) (scvi.external.Decipher attribute) (scvi.external.GIMVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI 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.external.VELOVI 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.BetaBinomial method) (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Poisson method) (scvi.distributions.ZeroInflatedNegativeBinomial method) id (scvi.autotune.AutotuneExperiment attribute) ignore_type() (scvi.utils.attrdict method) independent() (scvi.distributions.BetaBinomial method) infer_shapes() (scvi.distributions.BetaBinomial class method) (scvi.distributions.JaxNegativeBinomialMeanDisp class method) inference() (scvi.external.cellassign.CellAssignModule method) (scvi.external.contrastivevi.ContrastiveVAE method) (scvi.external.gimvi.JVAE method) (scvi.external.methylvi.METHYLVAE method) (scvi.external.mrvi.MRVAE method) (scvi.external.scbasset.ScBassetModule method) (scvi.external.stereoscope.RNADeconv method) (scvi.external.stereoscope.SpatialDeconv method) (scvi.external.tangram.TangramMapper method) (scvi.external.velovi.VELOVAE 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.VAEC method) init_embedding() (scvi.module.base.EmbeddingModuleMixin 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.Decipher attribute) (scvi.external.GIMVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI 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.external.VELOVI 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) learn_z_u_prior_scale (scvi.external.mrvi.MRVAE attribute) 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.Decipher class method) (scvi.external.GIMVI class method) (scvi.external.METHYLVI class method) (scvi.external.MRVI 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.external.VELOVI 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.METHYLVI class method) (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.Decipher static method) (scvi.external.GIMVI static method) (scvi.external.METHYLVI static method) (scvi.external.MRVI 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.external.VELOVI 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.BetaBinomial method) (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Poisson method) (scvi.distributions.ZeroInflatedNegativeBinomial method) log_with_mode() (scvi.train.SemiSupervisedTrainingPlan method) logging_dir (scvi._settings.ScviConfig attribute) (scvi.autotune.AutotuneExperiment 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.methylvi.METHYLVAE method) (scvi.external.mrvi.MRVAE method) (scvi.external.scbasset.ScBassetModule method) (scvi.external.stereoscope.RNADeconv method) (scvi.external.stereoscope.SpatialDeconv method) (scvi.external.tangram.TangramMapper method) (scvi.external.velovi.VELOVAE 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.BetaBinomial method) (scvi.distributions.JaxNegativeBinomialMeanDisp method) max_norm (scvi.nn.Embedding attribute) mean (scvi.distributions.BetaBinomial attribute) (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.Poisson attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) metadata (scvi.hub.HubModel attribute) METHYLVAE (class in scvi.external.methylvi) METHYLVI (class in scvi.external) metrics (scvi.autotune.AutotuneExperiment attribute) metrics_callback (scvi.autotune.AutotuneExperiment attribute) metrics_report (scvi.hub.HubModelCardHelper attribute) minified_data_type (scvi.model.base.BaseMinifiedModeModelClass attribute) (scvi.model.SCANVI attribute) (scvi.model.SCVI attribute) (scvi.model.TOTALVI attribute) (scvi.module.base.BaseMinifiedModeModuleClass attribute) minify_adata() (scvi.model.base.BaseMinifiedModeModelClass method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) minify_mudata() (scvi.model.TOTALVI 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.autotune.AutotuneExperiment attribute) (scvi.distributions.BetaBinomial attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.Poisson attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) model (scvi.hub.HubModel attribute) (scvi.module.AmortizedLDAPyroModule attribute) (scvi.module.base.PyroBaseModuleClass attribute) model() (scvi.external.decipher.DecipherPyroModule method) model_card (scvi.hub.HubModel attribute) model_cls (scvi.autotune.AutotuneExperiment 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_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) MOTIF_URLS (scvi.external.SCBASSET attribute) mouse_ob_dataset() (in module scvi.data) MRDeconv (class in scvi.module) MRVAE (class in scvi.external.mrvi) MRVI (class in scvi.external) 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.external.mrvi.MRVAE attribute) (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.external.mrvi.MRVAE attribute) (scvi.module.JaxVAE attribute) n_labels (scvi.external.mrvi.MRVAE attribute) n_latent (scvi.external.mrvi.MRVAE attribute) (scvi.module.JaxVAE attribute) n_latent_u (scvi.external.mrvi.MRVAE 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_per_sample (scvi.external.mrvi.MRVAE 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_sample (scvi.external.mrvi.MRVAE attribute) N_VARS_KEY (scvi.data.fields.LayerField attribute) name (scvi.autotune.AutotuneExperiment attribute) (scvi.dataloaders.DataSplitter attribute) (scvi.dataloaders.SemiSupervisedDataSplitter attribute) (scvi.external.mrvi.MRVAE 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) norm_type (scvi.nn.Embedding attribute) num_embeddings (scvi.nn.Embedding attribute) num_samples (scvi.autotune.AutotuneExperiment attribute) 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.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (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) (scvi.module.TOTALVAE 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) (scvi.train.SaveCheckpoint 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 padding_idx (scvi.nn.Embedding attribute) params (scvi.module.base.JaxBaseModuleClass attribute) parent (scvi.external.mrvi.MRVAE attribute) (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.BetaBinomial method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Poisson 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 (class in scvi.distributions) poisson_gene_selection() (in module scvi.data) POISSONVI (class in scvi.external) posterior_predictive_sample() (scvi.external.METHYLVI 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) 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) predictive_log_likelihood() (scvi.external.decipher.DecipherPyroModule 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.METHYLVI static method) (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) prepare_query_mudata() (scvi.external.METHYLVI static method) (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) px_kwargs (scvi.external.mrvi.MRVAE attribute) 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) Q qu_kwargs (scvi.external.mrvi.MRVAE attribute) qz_kwargs (scvi.external.mrvi.MRVAE 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_mudata() (scvi.hub.HubModel method) 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.Decipher class method) (scvi.external.GIMVI class method) (scvi.external.METHYLVI class method) (scvi.external.MRVI 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.external.VELOVI 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) remove_embedding() (scvi.module.base.EmbeddingModuleMixin method) reparametrized_params (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) replace() (scvi.module.base.LossOutput method) repo_name (scvi.hub.HubModel attribute) required (scvi.data.fields.CategoricalJointObsField attribute) (scvi.data.fields.CategoricalJointVarField attribute) (scvi.data.fields.NumericalJointObsField attribute) (scvi.data.fields.NumericalJointVarField attribute) required_rngs (scvi.external.mrvi.MRVAE attribute) (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() (scvi.distributions.BetaBinomial method) reshape_bernoulli() (scvi.module.AutoZIVAE method) resources (scvi.autotune.AutotuneExperiment attribute) result_grid (scvi.autotune.AutotuneExperiment 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.BetaBinomial method) (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Poisson method) (scvi.distributions.ZeroInflatedNegativeBinomial method) run_autotune() (in module scvi.autotune) rv (scvi.distributions.BetaBinomial attribute) S sample() (scvi.distributions.BetaBinomial method) (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Poisson method) (scvi.distributions.ZeroInflatedNegativeBinomial method) (scvi.external.cellassign.CellAssignModule method) (scvi.external.contrastivevi.ContrastiveVAE method) (scvi.external.methylvi.METHYLVAE method) (scvi.external.stereoscope.RNADeconv method) (scvi.external.stereoscope.SpatialDeconv method) (scvi.external.velovi.VELOVAE 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.BetaBinomial method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Poisson 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.Decipher method) (scvi.external.GIMVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI 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.external.VELOVI 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_grad_by_freq (scvi.nn.Embedding attribute) scale_observations (scvi.external.mrvi.MRVAE attribute) 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) scheduler (scvi.autotune.AutotuneExperiment attribute) scheduler_kwargs (scvi.autotune.AutotuneExperiment attribute) scope (scvi.external.mrvi.MRVAE attribute) (scvi.external.tangram.TangramMapper attribute) (scvi.module.base.JaxBaseModuleClass attribute) (scvi.module.JaxVAE attribute) score_parts() (scvi.distributions.BetaBinomial method) SCVI (class in scvi.model) scvi_version (scvi.hub.HubMetadata attribute) (scvi.hub.HubModelCardHelper attribute) ScviConfig (class in scvi._settings) search_space (scvi.autotune.AutotuneExperiment attribute) searcher (scvi.autotune.AutotuneExperiment attribute) searcher_kwargs (scvi.autotune.AutotuneExperiment attribute) seed (scvi._settings.ScviConfig attribute) (scvi.autotune.AutotuneExperiment attribute) SemiSupervisedDataLoader (class in scvi.dataloaders) SemiSupervisedDataSplitter (class in scvi.dataloaders) SemiSupervisedTrainingPlan (class in scvi.train) set_default_validate_args() (scvi.distributions.BetaBinomial static method) (scvi.distributions.JaxNegativeBinomialMeanDisp static method) (scvi.distributions.NegativeBinomial static method) (scvi.distributions.NegativeBinomialMixture static method) (scvi.distributions.Poisson 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.mrvi.MRVAE 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.Decipher class method) (scvi.external.GIMVI class method) (scvi.external.METHYLVI class method) (scvi.external.MRVI 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.external.VELOVI 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_method_args (scvi.autotune.AutotuneExperiment attribute) setup_method_name (scvi.autotune.AutotuneExperiment attribute) setup_mudata() (scvi.external.METHYLVI class method) (scvi.external.Tangram class method) (scvi.model.MULTIVI class method) (scvi.model.TOTALVI class method) shape() (scvi.distributions.BetaBinomial method) (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) sparse (scvi.nn.Embedding 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.BetaBinomial attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.Poisson 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.Decipher attribute) (scvi.external.GIMVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI 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.external.VELOVI 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.BetaBinomial attribute) (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.Poisson 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.Decipher attribute) (scvi.external.GIMVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI 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.external.VELOVI 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.Decipher method) (scvi.external.GIMVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI 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.external.VELOVI 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.BetaBinomial method) (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.Decipher method) (scvi.external.GIMVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI 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.external.VELOVI 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.Decipher attribute) (scvi.external.GIMVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI 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.external.VELOVI 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) Trainer (class in scvi.train) training (scvi.external.cellassign.CellAssignModule attribute) (scvi.external.contrastivevi.ContrastiveVAE attribute) (scvi.external.decipher.DecipherPyroModule attribute) (scvi.external.gimvi.JVAE attribute) (scvi.external.methylvi.METHYLVAE attribute) (scvi.external.mrvi.MRVAE attribute) (scvi.external.scbasset.ScBassetModule attribute) (scvi.external.stereoscope.RNADeconv attribute) (scvi.external.stereoscope.SpatialDeconv attribute) (scvi.external.tangram.TangramMapper attribute) (scvi.external.velovi.VELOVAE 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.DecoderSCVI attribute) (scvi.nn.Embedding 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) U u_prior_mixture (scvi.external.mrvi.MRVAE attribute) u_prior_mixture_k (scvi.external.mrvi.MRVAE attribute) u_prior_scale (scvi.external.mrvi.MRVAE attribute) 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_args() (scvi.distributions.JaxNegativeBinomialMeanDisp 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.Decipher attribute) (scvi.external.GIMVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI 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.external.VELOVI 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.BetaBinomial attribute) (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.Poisson attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) VarmField (class in scvi.data.fields) VELOVAE (class in scvi.external.velovi) VELOVI (class in scvi.external) verbosity (scvi._settings.ScviConfig attribute) view_anndata_setup() (scvi.external.CellAssign method) (scvi.external.ContrastiveVI method) (scvi.external.Decipher method) (scvi.external.GIMVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI 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.external.VELOVI 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.Decipher static method) (scvi.external.GIMVI static method) (scvi.external.METHYLVI static method) (scvi.external.MRVI 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.external.VELOVI 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) weight (scvi.nn.Embedding attribute) Z z_u_prior (scvi.external.mrvi.MRVAE attribute) z_u_prior_scale (scvi.external.mrvi.MRVAE attribute) zero_fraction() (scvi.criticism.PosteriorPredictiveCheck method) ZeroInflatedNegativeBinomial (class in scvi.distributions) zi_logits (scvi.distributions.ZeroInflatedNegativeBinomial attribute) zi_probs (scvi.distributions.ZeroInflatedNegativeBinomial attribute)
