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 accelerator (scvi.train.TrainerConfig attribute) adata (scvi.external.CellAssign attribute) (scvi.external.ContrastiveVI attribute) (scvi.external.CYTOVI attribute) (scvi.external.Decipher attribute) (scvi.external.DIAGVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JaxMRVI attribute) (scvi.external.METHYLANVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI attribute) (scvi.external.POISSONVI attribute) (scvi.external.RESOLVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SCBASSET attribute) (scvi.external.SCVIVA attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.SysVI attribute) (scvi.external.Tangram attribute) (scvi.external.TorchMRVI attribute) (scvi.external.TOTALANVI 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.mlxSCVI 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.CYTOVI attribute) (scvi.external.Decipher attribute) (scvi.external.DIAGVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JaxMRVI attribute) (scvi.external.METHYLANVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI attribute) (scvi.external.POISSONVI attribute) (scvi.external.RESOLVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SCBASSET attribute) (scvi.external.SCVIVA attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.SysVI attribute) (scvi.external.Tangram attribute) (scvi.external.TorchMRVI attribute) (scvi.external.TOTALANVI 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.mlxSCVI 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) adversarial_classifier (scvi.train.AdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) AdversarialTrainingPlan (class in scvi.train) AdversarialTrainingPlanConfig (class in scvi.train) allow_dotted_keys (scvi.utils.attrdict attribute) 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) (class in scvi.dataloaders) 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.Log1pNormal attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.Normal attribute) (scvi.distributions.Poisson attribute) (scvi.distributions.ZeroInflatedGamma attribute) (scvi.distributions.ZeroInflatedLogNormal 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) at_time() (scvi.external.decipher.utils.Trajectory 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) base_dist (scvi.distributions.ZeroInflatedLogNormal attribute) 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_labels (scvi.dataloaders.MappedCollectionDataModule attribute) batch_shape (scvi.distributions.BetaBinomial attribute) (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.Log1pNormal attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.Normal attribute) (scvi.distributions.Poisson attribute) (scvi.distributions.ZeroInflatedGamma attribute) (scvi.distributions.ZeroInflatedLogNormal attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) batch_size (scvi._settings.ScviConfig attribute) (scvi.dataloaders.AnnDataLoader attribute) (scvi.dataloaders.ConcatDataLoader attribute) (scvi.dataloaders.SemiSupervisedDataLoader attribute) BatchDistributedSampler (class in scvi.dataloaders) benchmark (scvi.train.TrainerConfig attribute) BetaBinomial (class in scvi.distributions) blocked (scvi.train.PyroTrainingPlanConfig attribute) brainlarge_dataset() (in module scvi.data) breast_cancer_dataset() (in module scvi.data) C calibration_error() (scvi.criticism.PosteriorPredictiveCheck method) CATEGORICAL_MAPPING_KEY (scvi.data.fields.CategoricalObsField attribute) (scvi.data.fields.CategoricalVarField attribute) (scvi.data.fields.LabelsWithUnlabeledObsField attribute) CategoricalJointObsField (class in scvi.data.fields) CategoricalJointVarField (class in scvi.data.fields) CategoricalObsField (class in scvi.data.fields) CategoricalVarField (class in scvi.data.fields) cdf() (scvi.distributions.BetaBinomial method) (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.Log1pNormal method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Normal method) (scvi.distributions.Poisson method) (scvi.distributions.ZeroInflatedGamma method) (scvi.distributions.ZeroInflatedLogNormal 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_val_every_n_epoch (scvi.train.TrainerConfig attribute) 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.MappedCollectionDataModule attribute) (scvi.dataloaders.SemiSupervisedDataSplitter attribute) (scvi.dataloaders.TileDBDataModule attribute) CHECKPOINT_HYPER_PARAMS_NAME (scvi.dataloaders.DataSplitter attribute) (scvi.dataloaders.MappedCollectionDataModule attribute) (scvi.dataloaders.SemiSupervisedDataSplitter attribute) (scvi.dataloaders.TileDBDataModule attribute) CHECKPOINT_HYPER_PARAMS_TYPE (scvi.dataloaders.DataSplitter attribute) (scvi.dataloaders.MappedCollectionDataModule attribute) (scvi.dataloaders.SemiSupervisedDataSplitter attribute) (scvi.dataloaders.TileDBDataModule attribute) checkpointing_monitor (scvi.train.TrainerConfig attribute) classification_loss (scvi.module.base.LossOutput attribute) classification_loss() (scvi.module.base.SupervisedModuleClass method) classification_ratio (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedTrainingPlanConfig attribute) Classifier (class in scvi.module) ClassifierTrainingPlan (class in scvi.train) ClassifierTrainingPlanConfig (class in scvi.train) classify() (scvi.external.methylvi.METHYLANVAE method) (scvi.external.totalanvi.TOTALANVAE method) (scvi.module.base.SupervisedModuleClass method) (scvi.module.VAEC method) classify_helper() (scvi.module.base.SupervisedModuleClass method) clear_cache (scvi.distributions.ZeroInflatedLogNormal attribute) close() (scvi.dataloaders.MappedCollectionDataModule method) cluster_locations (scvi.external.decipher.utils.Trajectory attribute) coefficient_of_variation() (scvi.criticism.PosteriorPredictiveCheck method) CollectionAdapter (class in scvi.dataloaders) 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) compile (scvi.train.AdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig attribute) compile_kwargs (scvi.train.AdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig attribute) composition_loss (scvi.external.scviva.NicheLossOutput attribute) compute_and_log_metrics() (scvi.train.SemiSupervisedTrainingPlan method) (scvi.train.TrainingPlan method) compute_dataset_dependent_priors() (scvi.external.RESOLVI 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) (scvi.external.mrvi_jax.JaxMRVAE method) (scvi.external.mrvi_torch.TorchMRVAE method) compute_imputed_gene_expression() (scvi.external.Decipher method) compute_local_statistics() (scvi.external.JaxMRVI method) (scvi.external.TorchMRVI 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.ClassifierTrainingPlan method) (scvi.train.JaxTrainingPlan method) (scvi.train.LowLevelPyroTrainingPlan method) (scvi.train.PyroTrainingPlan method) (scvi.train.SemiSupervisedAdversarialTrainingPlan method) (scvi.train.TrainingPlan method) confusion_coarse_celltypes() (scvi.model.CondSCVI method) conjugate_update() (scvi.distributions.BetaBinomial method) constrained (scvi.external.tangram.TangramMapper attribute) construct_custom_guidance_graph() (scvi.external.DIAGVI static method) ContrastiveDataSplitter (class in scvi.external.contrastivevi) 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.CYTOVI class method) (scvi.external.Decipher class method) (scvi.external.DIAGVI class method) (scvi.external.GIMVI class method) (scvi.external.JaxMRVI class method) (scvi.external.METHYLANVI class method) (scvi.external.METHYLVI class method) (scvi.external.MRVI class method) (scvi.external.POISSONVI class method) (scvi.external.RESOLVI class method) (scvi.external.RNAStereoscope class method) (scvi.external.SCAR class method) (scvi.external.SCBASSET class method) (scvi.external.SCVIVA class method) (scvi.external.SOLO class method) (scvi.external.SpatialStereoscope class method) (scvi.external.SysVI class method) (scvi.external.Tangram class method) (scvi.external.TorchMRVI class method) (scvi.external.TOTALANVI 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.mlxSCVI 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) cumulative_length (scvi.external.decipher.utils.Trajectory attribute) CytoVAE (class in scvi.external.cytovi) CYTOVI (class in scvi.external) D data (scvi.data.AnnTorchDataset attribute) (scvi.dataloaders.AnnTorchDataset attribute) data_is_annotated (scvi.hub.HubModelCardHelper attribute) data_is_minified (scvi.hub.HubModelCardHelper attribute) data_key (scvi.train.ClassifierTrainingPlanConfig attribute) data_modalities (scvi.hub.HubModelCardHelper attribute) data_registry (scvi.data.AnnDataManager attribute) data_registry() (scvi.external.CellAssign method) (scvi.external.ContrastiveVI method) (scvi.external.CYTOVI method) (scvi.external.Decipher method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.JaxMRVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.RESOLVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SCBASSET method) (scvi.external.SCVIVA method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.SysVI method) (scvi.external.Tangram method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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.mlxSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) 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) DecoderTOTALVI (class in scvi.nn) DEFAULT_MOTIF_DIR (scvi.external.SCBASSET attribute) default_root_dir (scvi.train.TrainerConfig attribute) deregister_manager() (scvi.external.CellAssign method) (scvi.external.ContrastiveVI method) (scvi.external.CYTOVI method) (scvi.external.Decipher method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.JaxMRVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.RESOLVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SCBASSET method) (scvi.external.SCVIVA method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.SysVI method) (scvi.external.Tangram method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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.mlxSCVI 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.CYTOVI attribute) (scvi.external.Decipher attribute) (scvi.external.decipher.DecipherPyroModule attribute) (scvi.external.DIAGVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JaxMRVI attribute) (scvi.external.METHYLANVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI attribute) (scvi.external.POISSONVI attribute) (scvi.external.RESOLVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SCBASSET attribute) (scvi.external.SCVIVA attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.SysVI attribute) (scvi.external.Tangram attribute) (scvi.external.TorchMRVI attribute) (scvi.external.TOTALANVI 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.mlxSCVI 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) devices (scvi.train.TrainerConfig attribute) DIAGVAE (class in scvi.external.diagvi) DIAGVI (class in scvi.external) dict_sum() (scvi.module.base.LossOutput static method) differential_abundance() (scvi.external.CellAssign method) (scvi.external.ContrastiveVI method) (scvi.external.CYTOVI method) (scvi.external.Decipher method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.JaxMRVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.RESOLVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SCBASSET method) (scvi.external.SCVIVA method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.SysVI method) (scvi.external.Tangram method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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.VAEMixin method) (scvi.model.CondSCVI method) (scvi.model.DestVI method) (scvi.model.JaxSCVI method) (scvi.model.LinearSCVI method) (scvi.model.mlxSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) differential_accessibility() (scvi.external.POISSONVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) differential_expression() (scvi.criticism.PosteriorPredictiveCheck method) (scvi.external.CellAssign method) (scvi.external.ContrastiveVI method) (scvi.external.CYTOVI method) (scvi.external.GIMVI method) (scvi.external.JaxMRVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.RESOLVI method) (scvi.external.SCAR method) (scvi.external.SCVIVA method) (scvi.external.SysVI method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI method) (scvi.model.AUTOZI method) (scvi.model.base.RNASeqMixin 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) differential_methylation() (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) differential_niche_abundance() (scvi.external.RESOLVI 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 early_stopping (scvi.train.TrainerConfig attribute) early_stopping_min_delta (scvi.train.TrainerConfig attribute) early_stopping_mode (scvi.train.TrainerConfig attribute) early_stopping_monitor (scvi.train.TrainerConfig attribute) early_stopping_patience (scvi.train.TrainerConfig attribute) early_stopping_warmup_epochs (scvi.train.TrainerConfig attribute) 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) enable_checkpointing (scvi.train.TrainerConfig attribute) enable_model_summary (scvi.train.TrainerConfig attribute) enable_progress_bar (scvi.train.TrainerConfig attribute) encode_graph() (scvi.external.diagvi.DIAGVAE method) Encoder (class in scvi.nn) encoder_n_hidden (scvi.external.mrvi_jax.JaxMRVAE attribute) encoder_n_layers (scvi.external.mrvi_jax.JaxMRVAE attribute) EncoderTOTALVI (class in scvi.nn) entropy() (scvi.distributions.BetaBinomial method) (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.Log1pNormal method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Normal method) (scvi.distributions.Poisson method) (scvi.distributions.ZeroInflatedGamma method) (scvi.distributions.ZeroInflatedLogNormal method) (scvi.distributions.ZeroInflatedNegativeBinomial method) enumerate_support() (scvi.distributions.BetaBinomial method) (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.Log1pNormal method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Normal method) (scvi.distributions.Poisson method) (scvi.distributions.ZeroInflatedGamma method) (scvi.distributions.ZeroInflatedLogNormal method) (scvi.distributions.ZeroInflatedNegativeBinomial method) eps (scvi.module.JaxVAE attribute) (scvi.train.ClassifierTrainingPlanConfig attribute) (scvi.train.JaxTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig 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.Log1pNormal attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.Normal attribute) (scvi.distributions.Poisson attribute) (scvi.distributions.ZeroInflatedGamma attribute) (scvi.distributions.ZeroInflatedLogNormal attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) expand() (scvi.distributions.BetaBinomial method) (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.Log1pNormal method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Normal method) (scvi.distributions.Poisson method) (scvi.distributions.ZeroInflatedGamma method) (scvi.distributions.ZeroInflatedLogNormal method) (scvi.distributions.ZeroInflatedNegativeBinomial method) expand_by() (scvi.distributions.BetaBinomial method) (scvi.distributions.JaxNegativeBinomialMeanDisp method) extend() (scvi.nn.Embedding class method) extra_categorical_covs (scvi.dataloaders.MappedCollectionDataModule attribute) (scvi.dataloaders.TileDBDataModule attribute) extra_continuous_covs (scvi.dataloaders.MappedCollectionDataModule attribute) (scvi.dataloaders.TileDBDataModule attribute) extra_kwargs (scvi.train.TrainerConfig attribute) extra_metrics (scvi.external.scviva.NicheLossOutput attribute) (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.external.sysvi.SysVAE method) (scvi.module.base.BaseModuleClass method) (scvi.module.base.PyroBaseModuleClass method) (scvi.module.Classifier method) (scvi.nn.Decoder method) (scvi.nn.DecoderSCVI method) (scvi.nn.DecoderTOTALVI method) (scvi.nn.Encoder method) (scvi.nn.EncoderTOTALVI method) (scvi.nn.FCLayers method) (scvi.nn.LinearDecoderSCVI method) (scvi.train.ClassifierTrainingPlan 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.MappedCollectionDataModule class method) (scvi.dataloaders.SemiSupervisedDataSplitter class method) (scvi.dataloaders.TileDBDataModule class method) from_dict() (scvi.external.decipher.utils.Trajectory static method) from_dir() (scvi.hub.HubMetadata class method) (scvi.hub.HubModelCardHelper class method) from_rna_model() (scvi.external.SpatialStereoscope class method) (scvi.model.DestVI class method) from_scvi_model() (scvi.external.SOLO class method) (scvi.model.SCANVI class method) from_totalvi_model() (scvi.external.TOTALANVI 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.cytovi.CytoVAE method) (scvi.external.diagvi.DIAGVAE method) (scvi.external.gimvi.JVAE method) (scvi.external.methylvi.METHYLVAE method) (scvi.external.mrvi.MRVAE method) (scvi.external.mrvi_jax.JaxMRVAE method) (scvi.external.mrvi_torch.TorchMRVAE method) (scvi.external.scbasset.ScBassetModule method) (scvi.external.scviva.nicheVAE method) (scvi.external.stereoscope.RNADeconv method) (scvi.external.stereoscope.SpatialDeconv method) (scvi.external.sysvi.SysVAE 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_aggregated_posterior() (scvi.external.CYTOVI method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.JaxMRVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.SCVIVA method) (scvi.external.SysVI method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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_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.CYTOVI method) (scvi.external.Decipher method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.JaxMRVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.RESOLVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SCBASSET method) (scvi.external.SCVIVA method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.SysVI method) (scvi.external.Tangram method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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.mlxSCVI 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.external.SCVIVA method) (scvi.external.TorchMRVI method) (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_composition_error() (scvi.external.SCVIVA method) get_ct_specific_expression() (scvi.external.stereoscope.SpatialDeconv 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.CYTOVI method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.SCVIVA method) (scvi.external.SysVI method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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_expression_for_ct() (scvi.model.DestVI method) get_feature_by_topic() (scvi.model.AmortizedLDA method) get_feature_correlation_matrix() (scvi.external.CellAssign method) (scvi.external.CYTOVI method) (scvi.external.GIMVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.SCVIVA method) (scvi.external.SysVI method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI method) (scvi.model.AUTOZI method) (scvi.model.base.RNASeqMixin method) (scvi.model.CondSCVI method) (scvi.model.LinearSCVI method) (scvi.model.PEAKVI 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_fine_celltypes() (scvi.model.DestVI method) get_from_registry() (scvi.data.AnnDataManager method) (scvi.external.CellAssign method) (scvi.external.ContrastiveVI method) (scvi.external.CYTOVI method) (scvi.external.Decipher method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.JaxMRVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.RESOLVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SCBASSET method) (scvi.external.SCVIVA method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.SysVI method) (scvi.external.Tangram method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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.mlxSCVI 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) get_gene_likelihood() (scvi.external.VELOVI method) get_importance_weights() (scvi.external.CellAssign method) (scvi.external.CYTOVI method) (scvi.external.GIMVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.SCVIVA method) (scvi.external.SysVI method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI method) (scvi.model.AUTOZI method) (scvi.model.base.RNASeqMixin method) (scvi.model.CondSCVI method) (scvi.model.LinearSCVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) get_imputed_values() (scvi.external.DIAGVI method) (scvi.external.GIMVI method) get_jit_inference_fn() (scvi.module.base.JaxBaseModuleClass method) get_latent_library_size() (scvi.external.CellAssign method) (scvi.external.ContrastiveVI method) (scvi.external.CYTOVI method) (scvi.external.GIMVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.SCVIVA method) (scvi.external.SysVI method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI method) (scvi.model.AUTOZI method) (scvi.model.base.RNASeqMixin method) (scvi.model.CondSCVI method) (scvi.model.LinearSCVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) get_latent_representation() (scvi.external.ContrastiveVI method) (scvi.external.CYTOVI method) (scvi.external.Decipher method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.JaxMRVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.POISSONVI method) (scvi.external.RESOLVI method) (scvi.external.SCAR method) (scvi.external.SCBASSET method) (scvi.external.SCVIVA method) (scvi.external.SysVI method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI method) (scvi.external.VELOVI method) (scvi.model.AmortizedLDA method) (scvi.model.AUTOZI method) (scvi.model.base.VAEMixin method) (scvi.model.CondSCVI method) (scvi.model.DestVI method) (scvi.model.JaxSCVI method) (scvi.model.LinearSCVI method) (scvi.model.mlxSCVI 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.CellAssign method) (scvi.external.CYTOVI method) (scvi.external.GIMVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.SCVIVA method) (scvi.external.SysVI method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI method) (scvi.model.AUTOZI method) (scvi.model.base.RNASeqMixin method) (scvi.model.CondSCVI method) (scvi.model.LinearSCVI method) (scvi.model.PEAKVI 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.JaxMRVI method) (scvi.external.TorchMRVI method) get_local_sample_representation() (scvi.external.JaxMRVI method) (scvi.external.TorchMRVI method) get_mapper_matrix() (scvi.external.Tangram method) get_marginal_ll() (scvi.external.CYTOVI method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.SCVIVA method) (scvi.external.SysVI method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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_neighbor_abundance() (scvi.external.RESOLVI method) get_niche_error() (scvi.external.SCVIVA method) get_normalized() (scvi.distributions.Log1pNormal method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Normal method) (scvi.distributions.Poisson method) (scvi.distributions.ZeroInflatedGamma method) (scvi.distributions.ZeroInflatedLogNormal method) (scvi.distributions.ZeroInflatedNegativeBinomial method) get_normalized_accessibility() (scvi.external.POISSONVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) get_normalized_expression() (scvi.external.CellAssign method) (scvi.external.ContrastiveVI method) (scvi.external.CYTOVI method) (scvi.external.Decipher method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.JaxMRVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.RESOLVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SCBASSET method) (scvi.external.SCVIVA method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.SysVI method) (scvi.external.Tangram method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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.RNASeqMixin method) (scvi.model.CondSCVI method) (scvi.model.DestVI method) (scvi.model.JaxSCVI method) (scvi.model.LinearSCVI method) (scvi.model.mlxSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) get_normalized_expression_importance() (scvi.external.RESOLVI method) get_normalized_function_name (scvi.external.CellAssign attribute) (scvi.external.ContrastiveVI attribute) (scvi.external.CYTOVI attribute) (scvi.external.Decipher attribute) (scvi.external.DIAGVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JaxMRVI attribute) (scvi.external.METHYLANVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI attribute) (scvi.external.POISSONVI attribute) (scvi.external.RESOLVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SCBASSET attribute) (scvi.external.SCVIVA attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.SysVI attribute) (scvi.external.Tangram attribute) (scvi.external.TorchMRVI attribute) (scvi.external.TOTALANVI 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.mlxSCVI attribute) (scvi.model.MULTIVI attribute) (scvi.model.PEAKVI attribute) (scvi.model.SCANVI attribute) (scvi.model.SCVI attribute) (scvi.model.TOTALVI attribute) get_normalized_methylation() (scvi.external.METHYLANVI method) (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.JaxMRVI method) (scvi.external.TorchMRVI 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) get_protein_background_mean() (scvi.external.TOTALANVI method) (scvi.model.TOTALVI method) get_protein_foreground_probability() (scvi.external.TOTALANVI method) (scvi.model.MULTIVI method) (scvi.model.TOTALVI method) get_px() (scvi.external.velovi.VELOVAE method) get_ranked_features() (scvi.external.METHYLANVI method) (scvi.external.TOTALANVI method) (scvi.model.base.SemisupervisedTrainingMixin method) (scvi.model.SCANVI method) get_rates() (scvi.external.VELOVI method) get_reconstruction_error() (scvi.external.CYTOVI method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.SCVIVA method) (scvi.external.SysVI method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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_logprobs() (scvi.external.CYTOVI method) get_sample_rate() (scvi.external.gimvi.JVAE method) get_scale_for_ct() (scvi.external.SpatialStereoscope method) (scvi.model.DestVI method) get_setup_arg() (scvi.external.CellAssign method) (scvi.external.ContrastiveVI method) (scvi.external.CYTOVI method) (scvi.external.Decipher method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.JaxMRVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.RESOLVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SCBASSET method) (scvi.external.SCVIVA method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.SysVI method) (scvi.external.Tangram method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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.mlxSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) get_specific_normalized_expression() (scvi.external.ContrastiveVI method) get_specific_normalized_methylation() (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) get_state_assignment() (scvi.external.VELOVI method) get_state_registry() (scvi.data.AnnDataManager method) (scvi.external.CellAssign method) (scvi.external.ContrastiveVI method) (scvi.external.CYTOVI method) (scvi.external.Decipher method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.JaxMRVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.RESOLVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SCBASSET method) (scvi.external.SCVIVA method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.SysVI method) (scvi.external.Tangram method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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.mlxSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) get_summary_stats() (scvi.data.fields.BaseAnnDataField method) (scvi.data.fields.BaseMuDataWrapperClass method) (scvi.data.fields.CategoricalJointObsField method) (scvi.data.fields.CategoricalJointVarField method) (scvi.data.fields.CategoricalObsField method) (scvi.data.fields.CategoricalVarField method) (scvi.data.fields.LabelsWithUnlabeledObsField method) (scvi.data.fields.LayerField method) (scvi.data.fields.MuDataCategoricalJointObsField method) (scvi.data.fields.MuDataCategoricalJointVarField method) (scvi.data.fields.MuDataCategoricalObsField method) (scvi.data.fields.MuDataCategoricalVarField method) (scvi.data.fields.MuDataLayerField method) (scvi.data.fields.MuDataNumericalJointObsField method) (scvi.data.fields.MuDataNumericalJointVarField method) (scvi.data.fields.MuDataNumericalObsField method) (scvi.data.fields.MuDataNumericalVarField method) (scvi.data.fields.MuDataObsmField method) (scvi.data.fields.MuDataProteinLayerField method) (scvi.data.fields.MuDataVarmField method) (scvi.data.fields.NumericalJointObsField method) (scvi.data.fields.NumericalJointVarField method) (scvi.data.fields.ObsmField method) (scvi.data.fields.ProteinObsmField method) (scvi.data.fields.StringUnsField method) (scvi.data.fields.VarmField method) get_tf_activity() (scvi.external.SCBASSET method) get_topic_distribution() (scvi.module.AmortizedLDAPyroModule method) get_type() (scvi.utils.attrdict method) get_vamp_prior() (scvi.model.CondSCVI method) get_var_names() (scvi.external.CellAssign method) (scvi.external.ContrastiveVI method) (scvi.external.CYTOVI method) (scvi.external.Decipher method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.JaxMRVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.RESOLVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SCBASSET method) (scvi.external.SCVIVA method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.SysVI method) (scvi.external.Tangram method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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.mlxSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) get_velocity() (scvi.external.VELOVI method) GIMVI (class in scvi.external) guide (scvi.external.resolvi.RESOLVAE attribute) (scvi.module.AmortizedLDAPyroModule attribute) (scvi.module.base.PyroBaseModuleClass attribute) guide() (scvi.external.decipher.DecipherPyroModule method) guide_simplified (scvi.external.resolvi.RESOLVAE attribute) H has_enumerate_support (scvi.distributions.BetaBinomial attribute) (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.Log1pNormal attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.Normal attribute) (scvi.distributions.Poisson attribute) (scvi.distributions.ZeroInflatedGamma attribute) (scvi.distributions.ZeroInflatedLogNormal attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) has_rsample (scvi.distributions.BetaBinomial attribute) (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.Log1pNormal attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.Normal attribute) (scvi.distributions.Poisson attribute) (scvi.distributions.ZeroInflatedGamma attribute) (scvi.distributions.ZeroInflatedLogNormal 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.CYTOVI attribute) (scvi.external.Decipher attribute) (scvi.external.DIAGVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JaxMRVI attribute) (scvi.external.METHYLANVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI attribute) (scvi.external.POISSONVI attribute) (scvi.external.RESOLVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SCBASSET attribute) (scvi.external.SCVIVA attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.SysVI attribute) (scvi.external.Tangram attribute) (scvi.external.TorchMRVI attribute) (scvi.external.TOTALANVI 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.mlxSCVI 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.MappedCollectionDataModule attribute) (scvi.dataloaders.SemiSupervisedDataSplitter attribute) (scvi.dataloaders.TileDBDataModule attribute) hparams_initial (scvi.dataloaders.DataSplitter attribute) (scvi.dataloaders.MappedCollectionDataModule attribute) (scvi.dataloaders.SemiSupervisedDataSplitter attribute) (scvi.dataloaders.TileDBDataModule 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.Log1pNormal method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Normal method) (scvi.distributions.Poisson method) (scvi.distributions.ZeroInflatedGamma method) (scvi.distributions.ZeroInflatedLogNormal method) (scvi.distributions.ZeroInflatedNegativeBinomial method) ignore_type() (scvi.utils.attrdict method) impute_categories_from_reference() (scvi.external.CYTOVI method) impute_rna_from_reference() (scvi.external.CYTOVI method) independent() (scvi.distributions.BetaBinomial method) infer_shapes() (scvi.distributions.BetaBinomial class method) (scvi.distributions.JaxNegativeBinomialMeanDisp class method) inference() (scvi.external.contrastivevi.ContrastiveVAE method) (scvi.external.cytovi.CytoVAE method) (scvi.external.diagvi.DIAGVAE method) (scvi.external.gimvi.JVAE method) (scvi.external.methylvi.METHYLVAE method) (scvi.external.mrvi.MRVAE method) (scvi.external.mrvi_jax.JaxMRVAE method) (scvi.external.mrvi_torch.TorchMRVAE method) (scvi.external.scbasset.ScBassetModule method) (scvi.external.stereoscope.RNADeconv method) (scvi.external.stereoscope.SpatialDeconv method) (scvi.external.sysvi.SysVAE 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) inference_dataloader() (scvi.dataloaders.MappedCollectionDataModule method) (scvi.dataloaders.TileDBDataModule 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.CYTOVI attribute) (scvi.external.Decipher attribute) (scvi.external.DIAGVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JaxMRVI attribute) (scvi.external.METHYLANVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI attribute) (scvi.external.POISSONVI attribute) (scvi.external.RESOLVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SCBASSET attribute) (scvi.external.SCVIVA attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.SysVI attribute) (scvi.external.Tangram attribute) (scvi.external.TorchMRVI attribute) (scvi.external.TOTALANVI 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.mlxSCVI 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) is_view (scvi.dataloaders.CollectionAdapter attribute) isbacked (scvi.dataloaders.CollectionAdapter 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) JaxMRVAE (class in scvi.external.mrvi_jax) JaxMRVI (class in scvi.external) JaxNegativeBinomialMeanDisp (class in scvi.distributions) JaxSCVI (class in scvi.model) JaxTrainingPlan (class in scvi.train) JaxTrainingPlanConfig (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 key_adversarial (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) keys() (scvi.utils.attrdict method) keys_and_dtypes (scvi.data.AnnTorchDataset attribute) (scvi.dataloaders.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 label_keys (scvi.dataloaders.MappedCollectionDataModule attribute) labels (scvi.dataloaders.MappedCollectionDataModule attribute) labels_key (scvi.train.ClassifierTrainingPlanConfig attribute) labels_mapping (scvi.dataloaders.TileDBDataModule attribute) 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_cycle_consistency() (scvi.external.sysvi.SysVAE static method) latent_kl_divergence() (scvi.external.contrastivevi.ContrastiveVAE static method) LayerField (class in scvi.data.fields) layers (scvi.dataloaders.CollectionAdapter attribute) LDVAE (class in scvi.module) learn_z_u_prior_scale (scvi.external.mrvi_jax.JaxMRVAE attribute) learning_rate_monitor (scvi.train.TrainerConfig attribute) library_kl_divergence() (scvi.external.contrastivevi.ContrastiveVAE method) license_info (scvi.hub.HubModelCardHelper attribute) LinearDecoderSCVI (class in scvi.nn) LinearSCVI (class in scvi.model) list_obs_plate_vars (scvi.external.resolvi.RESOLVAE attribute) (scvi.module.base.PyroBaseModuleClass attribute) load() (scvi.external.CellAssign class method) (scvi.external.ContrastiveVI class method) (scvi.external.CYTOVI class method) (scvi.external.Decipher class method) (scvi.external.DIAGVI class method) (scvi.external.GIMVI class method) (scvi.external.JaxMRVI class method) (scvi.external.METHYLANVI class method) (scvi.external.METHYLVI class method) (scvi.external.MRVI class method) (scvi.external.POISSONVI class method) (scvi.external.RESOLVI class method) (scvi.external.RNAStereoscope class method) (scvi.external.SCAR class method) (scvi.external.SCBASSET class method) (scvi.external.SCVIVA class method) (scvi.external.SOLO class method) (scvi.external.SpatialStereoscope class method) (scvi.external.SysVI class method) (scvi.external.Tangram class method) (scvi.external.TorchMRVI class method) (scvi.external.TOTALANVI 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.mlxSCVI 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.MappedCollectionDataModule method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.dataloaders.TileDBDataModule method) load_model() (scvi.hub.HubModel method) load_query_data() (scvi.external.CYTOVI class method) (scvi.external.METHYLANVI class method) (scvi.external.METHYLVI class method) (scvi.external.POISSONVI class method) (scvi.external.RESOLVI class method) (scvi.external.SCVIVA class method) (scvi.external.SysVI class method) (scvi.external.TorchMRVI class method) (scvi.external.TOTALANVI 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.CYTOVI static method) (scvi.external.Decipher static method) (scvi.external.DIAGVI static method) (scvi.external.GIMVI static method) (scvi.external.JaxMRVI static method) (scvi.external.METHYLANVI static method) (scvi.external.METHYLVI static method) (scvi.external.MRVI static method) (scvi.external.POISSONVI static method) (scvi.external.RESOLVI static method) (scvi.external.RNAStereoscope static method) (scvi.external.SCAR static method) (scvi.external.SCBASSET static method) (scvi.external.SCVIVA static method) (scvi.external.SOLO static method) (scvi.external.SpatialStereoscope static method) (scvi.external.SysVI static method) (scvi.external.Tangram static method) (scvi.external.TorchMRVI static method) (scvi.external.TOTALANVI 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.mlxSCVI 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.MappedCollectionDataModule method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.dataloaders.TileDBDataModule method) (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) (scvi.module.base.JaxBaseModuleClass method) loc (scvi.distributions.ZeroInflatedLogNormal attribute) local_dir (scvi.hub.HubModel attribute) lock() (scvi.utils.attrdict method) Log1pNormal (class in scvi.distributions) log_every_n_steps (scvi.train.TrainerConfig attribute) log_prob() (scvi.distributions.BetaBinomial method) (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.Log1pNormal method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Normal method) (scvi.distributions.Poisson method) (scvi.distributions.ZeroInflatedGamma method) (scvi.distributions.ZeroInflatedLogNormal method) (scvi.distributions.ZeroInflatedNegativeBinomial method) log_save_dir (scvi.train.TrainerConfig attribute) log_with_mode() (scvi.train.SemiSupervisedTrainingPlan method) logger (scvi.train.TrainerConfig attribute) logging_dir (scvi._settings.ScviConfig attribute) logits (scvi.module.base.LossOutput attribute) loss (scvi.external.scviva.NicheLossOutput attribute) (scvi.module.base.LossOutput attribute) loss() (scvi.external.cellassign.CellAssignModule method) (scvi.external.contrastivevi.ContrastiveVAE method) (scvi.external.cytovi.CytoVAE method) (scvi.external.diagvi.DIAGVAE method) (scvi.external.gimvi.JVAE method) (scvi.external.methylvi.METHYLANVAE method) (scvi.external.methylvi.METHYLVAE method) (scvi.external.mrvi.MRVAE method) (scvi.external.mrvi_jax.JaxMRVAE method) (scvi.external.mrvi_torch.TorchMRVAE method) (scvi.external.scbasset.ScBassetModule method) (scvi.external.scviva.nicheVAE method) (scvi.external.stereoscope.RNADeconv method) (scvi.external.stereoscope.SpatialDeconv method) (scvi.external.sysvi.SysVAE method) (scvi.external.tangram.TangramMapper method) (scvi.external.totalanvi.TOTALANVAE 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) (scvi.train.SemiSupervisedAdversarialTrainingPlan method) loss_fn (scvi.train.LowLevelPyroTrainingPlanConfig attribute) (scvi.train.PyroTrainingPlanConfig attribute) loss_kwargs (scvi.train.AdversarialTrainingPlanConfig attribute) (scvi.train.JaxTrainingPlanConfig attribute) (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig attribute) LossOutput (class in scvi.module.base) LoudEarlyStopping (class in scvi.train) LowLevelPyroTrainingPlan (class in scvi.train) LowLevelPyroTrainingPlanConfig (class in scvi.train) lr (scvi.train.AdversarialTrainingPlanConfig attribute) (scvi.train.ClassifierTrainingPlanConfig attribute) (scvi.train.JaxTrainingPlanConfig attribute) (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig attribute) lr_factor (scvi.train.AdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig attribute) lr_min (scvi.train.AdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig attribute) lr_patience (scvi.train.AdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig attribute) lr_scheduler_metric (scvi.train.AdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig attribute) lr_threshold (scvi.train.AdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig attribute) M MappedCollectionDataModule (class in scvi.dataloaders) MAPPINGS_KEY (scvi.data.fields.CategoricalJointObsField attribute) (scvi.data.fields.CategoricalJointVarField attribute) marginal_ll() (scvi.external.cytovi.CytoVAE method) (scvi.module.TOTALVAE method) (scvi.module.VAE method) mask() (scvi.distributions.BetaBinomial method) (scvi.distributions.JaxNegativeBinomialMeanDisp method) max_epochs (scvi.train.TrainerConfig attribute) max_kl_weight (scvi.train.TrainingPlanConfig attribute) max_norm (scvi.nn.Embedding attribute) (scvi.train.JaxTrainingPlanConfig attribute) mean (scvi.distributions.BetaBinomial attribute) (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.Log1pNormal attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.Normal attribute) (scvi.distributions.Poisson attribute) (scvi.distributions.ZeroInflatedGamma attribute) (scvi.distributions.ZeroInflatedLogNormal attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) metadata (scvi.hub.HubModel attribute) METHYLANVAE (class in scvi.external.methylvi) METHYLANVI (class in scvi.external) METHYLVAE (class in scvi.external.methylvi) METHYLVI (class in scvi.external) metrics_report (scvi.hub.HubModelCardHelper attribute) min_kl_weight (scvi.train.TrainingPlanConfig attribute) minified_data_type (scvi.external.MRVI attribute) (scvi.external.SCVIVA attribute) (scvi.external.TorchMRVI attribute) (scvi.external.TOTALANVI attribute) (scvi.model.base.BaseMinifiedModeModelClass attribute) (scvi.model.LinearSCVI attribute) (scvi.model.MULTIVI attribute) (scvi.model.SCANVI attribute) (scvi.model.SCVI attribute) (scvi.model.TOTALVI attribute) (scvi.module.base.BaseMinifiedModeModuleClass attribute) minify_adata() (scvi.external.MRVI method) (scvi.external.SCVIVA method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI method) (scvi.model.base.BaseMinifiedModeModelClass method) (scvi.model.LinearSCVI method) (scvi.model.MULTIVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) minify_mudata() (scvi.external.TOTALANVI method) (scvi.model.MULTIVI method) (scvi.model.TOTALVI method) mixture_probs (scvi.distributions.NegativeBinomialMixture attribute) mlflow_set_experiment (scvi._settings.ScviConfig attribute) mlflow_set_tracking_uri (scvi._settings.ScviConfig attribute) mlxSCVI (class in scvi.model) mod_key (scvi.data.fields.BaseAnnDataField attribute) (scvi.data.fields.BaseMuDataWrapperClass attribute) (scvi.data.fields.CategoricalJointObsField attribute) (scvi.data.fields.CategoricalJointVarField attribute) (scvi.data.fields.CategoricalObsField attribute) (scvi.data.fields.CategoricalVarField attribute) (scvi.data.fields.LabelsWithUnlabeledObsField attribute) (scvi.data.fields.LayerField attribute) (scvi.data.fields.MuDataCategoricalJointObsField attribute) (scvi.data.fields.MuDataCategoricalJointVarField attribute) (scvi.data.fields.MuDataCategoricalObsField attribute) (scvi.data.fields.MuDataCategoricalVarField attribute) (scvi.data.fields.MuDataLayerField attribute) (scvi.data.fields.MuDataNumericalJointObsField attribute) (scvi.data.fields.MuDataNumericalJointVarField attribute) (scvi.data.fields.MuDataNumericalObsField attribute) (scvi.data.fields.MuDataNumericalVarField attribute) (scvi.data.fields.MuDataObsmField attribute) (scvi.data.fields.MuDataProteinLayerField attribute) (scvi.data.fields.MuDataVarmField attribute) (scvi.data.fields.NumericalJointObsField attribute) (scvi.data.fields.NumericalJointVarField attribute) (scvi.data.fields.ObsmField attribute) (scvi.data.fields.ProteinObsmField attribute) (scvi.data.fields.StringUnsField attribute) (scvi.data.fields.VarmField attribute) mode (scvi.distributions.BetaBinomial attribute) (scvi.distributions.Log1pNormal attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.Normal attribute) (scvi.distributions.Poisson attribute) (scvi.distributions.ZeroInflatedGamma attribute) (scvi.distributions.ZeroInflatedLogNormal attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) model (scvi.external.resolvi.RESOLVAE attribute) (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_name (scvi.hub.HubMetadata attribute) (scvi.hub.HubModelCardHelper attribute) model_corrected (scvi.external.resolvi.RESOLVAE 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_residuals (scvi.external.resolvi.RESOLVAE attribute) model_setup_anndata_args (scvi.hub.HubModelCardHelper attribute) model_simplified (scvi.external.resolvi.RESOLVAE attribute) model_summary_stats (scvi.hub.HubModelCardHelper attribute) model_unconditioned (scvi.external.resolvi.RESOLVAE attribute) MOTIF_URLS (scvi.external.SCBASSET attribute) mouse_ob_dataset() (in module scvi.data) MRDeconv (class in scvi.module) MRVAE (in module 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.dataloaders.MappedCollectionDataModule attribute) (scvi.dataloaders.TileDBDataModule attribute) (scvi.external.mrvi_jax.JaxMRVAE attribute) (scvi.module.JaxVAE attribute) n_cats_per_cov (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_continuous_cov (scvi.module.JaxVAE attribute) n_epochs_kl_warmup (scvi.train.AdversarialTrainingPlanConfig attribute) (scvi.train.JaxTrainingPlanConfig attribute) (scvi.train.LowLevelPyroTrainingPlanConfig attribute) (scvi.train.PyroTrainingPlanConfig attribute) (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig attribute) n_hidden (scvi.module.JaxVAE attribute) n_input (scvi.external.mrvi_jax.JaxMRVAE attribute) (scvi.module.JaxVAE attribute) n_labels (scvi.dataloaders.MappedCollectionDataModule attribute) (scvi.dataloaders.TileDBDataModule attribute) (scvi.external.mrvi_jax.JaxMRVAE attribute) n_latent (scvi.external.mrvi_jax.JaxMRVAE attribute) (scvi.module.JaxVAE attribute) n_latent_u (scvi.external.mrvi_jax.JaxMRVAE attribute) n_layers (scvi.module.JaxVAE attribute) n_obs (scvi.dataloaders.MappedCollectionDataModule attribute) (scvi.dataloaders.TileDBDataModule attribute) N_OBS_KEY (scvi.data.fields.LayerField attribute) n_obs_minibatch (scvi.module.base.LossOutput attribute) n_obs_per_sample (scvi.external.mrvi_jax.JaxMRVAE 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_points (scvi.external.decipher.utils.Trajectory attribute) n_sample (scvi.external.mrvi_jax.JaxMRVAE attribute) n_samples (scvi.dataloaders.MappedCollectionDataModule attribute) (scvi.dataloaders.TileDBDataModule attribute) n_steps_kl_warmup (scvi.train.AdversarialTrainingPlanConfig attribute) (scvi.train.JaxTrainingPlanConfig attribute) (scvi.train.LowLevelPyroTrainingPlanConfig attribute) (scvi.train.PyroTrainingPlanConfig attribute) (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig attribute) n_vars (scvi.dataloaders.MappedCollectionDataModule attribute) (scvi.dataloaders.TileDBDataModule attribute) N_VARS_KEY (scvi.data.fields.LayerField attribute) name (scvi.dataloaders.DataSplitter attribute) (scvi.dataloaders.MappedCollectionDataModule attribute) (scvi.dataloaders.SemiSupervisedDataSplitter attribute) (scvi.dataloaders.TileDBDataModule attribute) (scvi.external.mrvi_jax.JaxMRVAE 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) niche_loss (scvi.external.scviva.NicheLossOutput attribute) NicheLossOutput (class in scvi.external.scviva) nicheVAE (class in scvi.external.scviva) norm_type (scvi.nn.Embedding attribute) Normal (class in scvi.distributions) num_embeddings (scvi.nn.Embedding attribute) num_sanity_val_steps (scvi.train.TrainerConfig 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.MappedCollectionDataModule method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.dataloaders.TileDBDataModule method) on_before_backward() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_before_batch_transfer() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.MappedCollectionDataModule method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.dataloaders.TileDBDataModule 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_epoch (scvi.train.TrainingPlanConfig attribute) on_exception() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.MappedCollectionDataModule method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.dataloaders.TileDBDataModule method) (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) (scvi.train.SaveCheckpoint 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.base.SupervisedModuleClass 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_step (scvi.train.TrainingPlanConfig attribute) 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) (scvi.train.SaveCheckpoint 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.SaveCheckpoint method) (scvi.train.ScibCallback method) on_train_epoch_end() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) (scvi.train.AdversarialTrainingPlan method) (scvi.train.LowLevelPyroTrainingPlan method) (scvi.train.SemiSupervisedAdversarialTrainingPlan 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) 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) (scvi.train.ScibCallback method) on_validation_epoch_end() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) (scvi.train.AdversarialTrainingPlan method) (scvi.train.SemiSupervisedAdversarialTrainingPlan 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) optim (scvi.train.LowLevelPyroTrainingPlanConfig attribute) (scvi.train.PyroTrainingPlanConfig attribute) optim_kwargs (scvi.train.LowLevelPyroTrainingPlanConfig attribute) (scvi.train.PyroTrainingPlanConfig attribute) optimizer (scvi.train.AdversarialTrainingPlanConfig attribute) (scvi.train.ClassifierTrainingPlanConfig attribute) (scvi.train.JaxTrainingPlanConfig attribute) (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig attribute) optimizer_creator (scvi.train.AdversarialTrainingPlanConfig attribute) (scvi.train.JaxTrainingPlanConfig attribute) (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig attribute) 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_jax.JaxMRVAE 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.Log1pNormal method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Normal method) (scvi.distributions.Poisson method) (scvi.distributions.ZeroInflatedGamma method) (scvi.distributions.ZeroInflatedLogNormal 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.CellAssign method) (scvi.external.CYTOVI method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.METHYLVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.SCVIVA method) (scvi.external.SysVI method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI method) (scvi.model.AUTOZI method) (scvi.model.base.RNASeqMixin method) (scvi.model.CondSCVI method) (scvi.model.LinearSCVI method) (scvi.model.PEAKVI 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.METHYLANVI method) (scvi.external.RESOLVI method) (scvi.external.SOLO method) (scvi.external.TOTALANVI method) (scvi.model.base.SemisupervisedTrainingMixin method) (scvi.model.CondSCVI method) (scvi.model.SCANVI method) predict_celltype() (scvi.external.DIAGVI method) predict_dataloader() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.MappedCollectionDataModule method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.dataloaders.TileDBDataModule method) predict_neighborhood() (scvi.external.SCVIVA method) predict_niche_activation() (scvi.external.SCVIVA 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.MappedCollectionDataModule method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.dataloaders.TileDBDataModule method) prepare_query_anndata() (scvi.external.CYTOVI static method) (scvi.external.METHYLANVI static method) (scvi.external.METHYLVI static method) (scvi.external.POISSONVI static method) (scvi.external.RESOLVI static method) (scvi.external.SCVIVA static method) (scvi.external.SysVI static method) (scvi.external.TorchMRVI static method) (scvi.external.TOTALANVI 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.CYTOVI static method) (scvi.external.METHYLANVI static method) (scvi.external.METHYLVI static method) (scvi.external.POISSONVI static method) (scvi.external.RESOLVI static method) (scvi.external.SCVIVA static method) (scvi.external.SysVI static method) (scvi.external.TorchMRVI static method) (scvi.external.TOTALANVI 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_scib_autotune() (scvi.train.TrainingPlan method) preprocessing_anndata() (scvi.external.SCVIVA static method) preprocessing_query_anndata() (scvi.external.SCVIVA 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_refresh_rate (scvi.train.TrainerConfig attribute) 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_jax.JaxMRVAE 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) PyroTrainingPlanConfig (class in scvi.train) pytree_aux_fields (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) pytree_data_fields (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) Q qu_kwargs (scvi.external.mrvi_jax.JaxMRVAE attribute) qz_kwargs (scvi.external.mrvi_jax.JaxMRVAE attribute) R random_select_batch() (scvi.external.sysvi.SysVAE method) 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) reduce_lr_on_plateau (scvi.train.AdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig 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.CYTOVI class method) (scvi.external.Decipher class method) (scvi.external.DIAGVI class method) (scvi.external.GIMVI class method) (scvi.external.JaxMRVI class method) (scvi.external.METHYLANVI class method) (scvi.external.METHYLVI class method) (scvi.external.MRVI class method) (scvi.external.POISSONVI class method) (scvi.external.RESOLVI class method) (scvi.external.RNAStereoscope class method) (scvi.external.SCAR class method) (scvi.external.SCBASSET class method) (scvi.external.SCVIVA class method) (scvi.external.SOLO class method) (scvi.external.SpatialStereoscope class method) (scvi.external.SysVI class method) (scvi.external.Tangram class method) (scvi.external.TorchMRVI class method) (scvi.external.TOTALANVI 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.mlxSCVI 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) (scvi.dataloaders.AnnTorchDataset attribute) registry (scvi.data.AnnDataManager attribute) (scvi.dataloaders.MappedCollectionDataModule attribute) (scvi.dataloaders.TileDBDataModule attribute) (scvi.external.CellAssign attribute) (scvi.external.ContrastiveVI attribute) (scvi.external.CYTOVI attribute) (scvi.external.Decipher attribute) (scvi.external.DIAGVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JaxMRVI attribute) (scvi.external.METHYLANVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI attribute) (scvi.external.POISSONVI attribute) (scvi.external.RESOLVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SCBASSET attribute) (scvi.external.SCVIVA attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.SysVI attribute) (scvi.external.Tangram attribute) (scvi.external.TorchMRVI attribute) (scvi.external.TOTALANVI 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.mlxSCVI attribute) (scvi.model.MULTIVI attribute) (scvi.model.PEAKVI attribute) (scvi.model.SCANVI attribute) (scvi.model.SCVI attribute) (scvi.model.TOTALVI 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) remove_ignored_hparams() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.MappedCollectionDataModule method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.dataloaders.TileDBDataModule method) reparameterize_transformation() (scvi.nn.EncoderTOTALVI method) reparametrized_params (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) 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_jax.JaxMRVAE 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) RESOLVAE (class in scvi.external.resolvi) RESOLVI (class in scvi.external) 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.Log1pNormal method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Normal method) (scvi.distributions.Poisson method) (scvi.distributions.ZeroInflatedGamma method) (scvi.distributions.ZeroInflatedLogNormal method) (scvi.distributions.ZeroInflatedNegativeBinomial method) run_autotune() (in module scvi.autotune) run_id (scvi.external.CellAssign attribute) (scvi.external.ContrastiveVI attribute) (scvi.external.CYTOVI attribute) (scvi.external.Decipher attribute) (scvi.external.DIAGVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JaxMRVI attribute) (scvi.external.METHYLANVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI attribute) (scvi.external.POISSONVI attribute) (scvi.external.RESOLVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SCBASSET attribute) (scvi.external.SCVIVA attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.SysVI attribute) (scvi.external.Tangram attribute) (scvi.external.TorchMRVI attribute) (scvi.external.TOTALANVI 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.mlxSCVI attribute) (scvi.model.MULTIVI attribute) (scvi.model.PEAKVI attribute) (scvi.model.SCANVI attribute) (scvi.model.SCVI attribute) (scvi.model.TOTALVI attribute) run_name (scvi.external.CellAssign attribute) (scvi.external.ContrastiveVI attribute) (scvi.external.CYTOVI attribute) (scvi.external.Decipher attribute) (scvi.external.DIAGVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JaxMRVI attribute) (scvi.external.METHYLANVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI attribute) (scvi.external.POISSONVI attribute) (scvi.external.RESOLVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SCBASSET attribute) (scvi.external.SCVIVA attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.SysVI attribute) (scvi.external.Tangram attribute) (scvi.external.TorchMRVI attribute) (scvi.external.TOTALANVI 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.mlxSCVI attribute) (scvi.model.MULTIVI attribute) (scvi.model.PEAKVI attribute) (scvi.model.SCANVI attribute) (scvi.model.SCVI attribute) (scvi.model.TOTALVI attribute) rv (scvi.distributions.BetaBinomial attribute) S sample() (scvi.distributions.BetaBinomial method) (scvi.distributions.JaxNegativeBinomialMeanDisp method) (scvi.distributions.Log1pNormal method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Normal method) (scvi.distributions.Poisson method) (scvi.distributions.ZeroInflatedGamma method) (scvi.distributions.ZeroInflatedLogNormal method) (scvi.distributions.ZeroInflatedNegativeBinomial method) (scvi.external.cellassign.CellAssignModule method) (scvi.external.contrastivevi.ContrastiveVAE method) (scvi.external.cytovi.CytoVAE method) (scvi.external.diagvi.DIAGVAE method) (scvi.external.methylvi.METHYLVAE method) (scvi.external.stereoscope.RNADeconv method) (scvi.external.stereoscope.SpatialDeconv method) (scvi.external.sysvi.SysVAE 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_keys (scvi.dataloaders.MappedCollectionDataModule attribute) sample_n() (scvi.distributions.BetaBinomial method) (scvi.distributions.Log1pNormal method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.Normal method) (scvi.distributions.Poisson method) (scvi.distributions.ZeroInflatedGamma method) (scvi.distributions.ZeroInflatedLogNormal method) (scvi.distributions.ZeroInflatedNegativeBinomial method) sample_posterior() (scvi.external.RESOLVI method) (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) samples (scvi.dataloaders.MappedCollectionDataModule attribute) samples_mapping (scvi.dataloaders.TileDBDataModule attribute) save() (scvi.external.CellAssign method) (scvi.external.ContrastiveVI method) (scvi.external.CYTOVI method) (scvi.external.Decipher method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.JaxMRVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.RESOLVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SCBASSET method) (scvi.external.SCVIVA method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.SysVI method) (scvi.external.Tangram method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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.mlxSCVI 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.MappedCollectionDataModule method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.dataloaders.TileDBDataModule method) SaveCheckpoint (class in scvi.train) scale (scvi.distributions.ZeroInflatedLogNormal attribute) scale_adversarial_loss (scvi.train.AdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) scale_elbo (scvi.train.LowLevelPyroTrainingPlanConfig attribute) (scvi.train.PyroTrainingPlanConfig attribute) scale_grad_by_freq (scvi.nn.Embedding attribute) scale_observations (scvi.external.mrvi_jax.JaxMRVAE 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) ScibCallback (class in scvi.train) scope (scvi.external.mrvi_jax.JaxMRVAE 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) SCVIVA (class in scvi.external) seed (scvi._settings.ScviConfig attribute) SemiSupervisedAdversarialTrainingPlan (class in scvi.train) SemiSupervisedAdversarialTrainingPlanConfig (class in scvi.train) SemiSupervisedDataLoader (class in scvi.dataloaders) SemiSupervisedDataSplitter (class in scvi.dataloaders) SemisupervisedTrainingMixin (class in scvi.model.base) SemiSupervisedTrainingPlan (class in scvi.train) SemiSupervisedTrainingPlanConfig (class in scvi.train) set_default_validate_args() (scvi.distributions.BetaBinomial static method) (scvi.distributions.JaxNegativeBinomialMeanDisp static method) (scvi.distributions.Log1pNormal static method) (scvi.distributions.NegativeBinomial static method) (scvi.distributions.NegativeBinomialMixture static method) (scvi.distributions.Normal static method) (scvi.distributions.Poisson static method) (scvi.distributions.ZeroInflatedGamma static method) (scvi.distributions.ZeroInflatedLogNormal static method) (scvi.distributions.ZeroInflatedNegativeBinomial static method) set_epoch() (scvi.dataloaders.BatchDistributedSampler method) set_online_update_hooks() (scvi.nn.FCLayers method) set_train_state() (scvi.train.JaxTrainingPlan method) setup() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.MappedCollectionDataModule method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.dataloaders.TileDBDataModule method) (scvi.external.contrastivevi.ContrastiveDataSplitter method) (scvi.external.mrvi_jax.JaxMRVAE 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.CYTOVI class method) (scvi.external.Decipher class method) (scvi.external.DIAGVI class method) (scvi.external.GIMVI class method) (scvi.external.JaxMRVI class method) (scvi.external.METHYLANVI class method) (scvi.external.METHYLVI class method) (scvi.external.MRVI class method) (scvi.external.POISSONVI class method) (scvi.external.RESOLVI class method) (scvi.external.RNAStereoscope class method) (scvi.external.SCAR class method) (scvi.external.SCBASSET class method) (scvi.external.SCVIVA class method) (scvi.external.SOLO class method) (scvi.external.SpatialStereoscope class method) (scvi.external.SysVI class method) (scvi.external.Tangram class method) (scvi.external.TorchMRVI class method) (scvi.external.TOTALANVI 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.mlxSCVI class method) (scvi.model.MULTIVI class method) (scvi.model.PEAKVI class method) (scvi.model.SCANVI class method) (scvi.model.SCVI class method) (scvi.model.TOTALVI class method) setup_anndata_dsp (in module scvi.utils) setup_mudata() (scvi.external.DIAGVI class method) (scvi.external.METHYLANVI class method) (scvi.external.METHYLVI class method) (scvi.external.Tangram class method) (scvi.external.TOTALANVI class method) (scvi.model.MULTIVI class method) (scvi.model.TOTALVI class method) shap_adata_predict() (scvi.external.METHYLANVI method) (scvi.external.TOTALANVI method) (scvi.model.base.SemisupervisedTrainingMixin method) (scvi.model.SCANVI method) shap_predict() (scvi.external.METHYLANVI method) (scvi.external.TOTALANVI method) (scvi.model.base.SemisupervisedTrainingMixin method) (scvi.model.SCANVI method) shape() (scvi.distributions.BetaBinomial method) (scvi.distributions.JaxNegativeBinomialMeanDisp method) simple_progress_bar (scvi.train.TrainerConfig attribute) 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) SPECIAL_ATTRS (scvi.dataloaders.CollectionAdapter attribute) spleen_lymph_cite_seq() (in module scvi.data) split_seed (scvi.dataloaders.TileDBDataModule attribute) state (scvi.module.base.JaxBaseModuleClass attribute) state_dict() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.MappedCollectionDataModule method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.dataloaders.TileDBDataModule 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.Log1pNormal attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.Normal attribute) (scvi.distributions.Poisson attribute) (scvi.distributions.ZeroInflatedGamma attribute) (scvi.distributions.ZeroInflatedLogNormal 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.CYTOVI attribute) (scvi.external.Decipher attribute) (scvi.external.DIAGVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JaxMRVI attribute) (scvi.external.METHYLANVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI attribute) (scvi.external.POISSONVI attribute) (scvi.external.RESOLVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SCBASSET attribute) (scvi.external.SCVIVA attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.SysVI attribute) (scvi.external.Tangram attribute) (scvi.external.TorchMRVI attribute) (scvi.external.TOTALANVI 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.mlxSCVI attribute) (scvi.model.MULTIVI attribute) (scvi.model.PEAKVI attribute) (scvi.model.SCANVI attribute) (scvi.model.SCVI attribute) (scvi.model.TOTALVI attribute) SupervisedModuleClass (class in scvi.module.base) support (scvi.distributions.BetaBinomial attribute) (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.Log1pNormal attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.Normal attribute) (scvi.distributions.Poisson attribute) (scvi.distributions.ZeroInflatedGamma attribute) (scvi.distributions.ZeroInflatedLogNormal attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) synthetic_iid() (in module scvi.data) SysVAE (class in scvi.external.sysvi) SysVI (class in scvi.external) 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.MappedCollectionDataModule method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.dataloaders.TileDBDataModule method) (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) (scvi.train.LoudEarlyStopping method) test_dataloader() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.MappedCollectionDataModule method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.dataloaders.TileDBDataModule method) (scvi.external.contrastivevi.ContrastiveDataSplitter method) test_indices (scvi.external.CellAssign attribute) (scvi.external.ContrastiveVI attribute) (scvi.external.CYTOVI attribute) (scvi.external.Decipher attribute) (scvi.external.DIAGVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JaxMRVI attribute) (scvi.external.METHYLANVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI attribute) (scvi.external.POISSONVI attribute) (scvi.external.RESOLVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SCBASSET attribute) (scvi.external.SCVIVA attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.SysVI attribute) (scvi.external.Tangram attribute) (scvi.external.TorchMRVI attribute) (scvi.external.TOTALANVI 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.mlxSCVI attribute) (scvi.model.MULTIVI attribute) (scvi.model.PEAKVI attribute) (scvi.model.SCANVI attribute) (scvi.model.SCVI attribute) (scvi.model.TOTALVI attribute) TileDBDataModule (class in scvi.dataloaders) 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.CYTOVI method) (scvi.external.Decipher method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.JaxMRVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.RESOLVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SCBASSET method) (scvi.external.SCVIVA method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.SysVI method) (scvi.external.Tangram method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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.mlxSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) to_dict() (scvi.external.decipher.utils.Trajectory method) (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_kwargs() (scvi.train.AdversarialTrainingPlanConfig method) (scvi.train.ClassifierTrainingPlanConfig method) (scvi.train.JaxTrainingPlanConfig method) (scvi.train.LowLevelPyroTrainingPlanConfig method) (scvi.train.PyroTrainingPlanConfig method) (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig method) (scvi.train.SemiSupervisedTrainingPlanConfig method) (scvi.train.TrainerConfig method) (scvi.train.TrainingPlanConfig method) to_yaml() (scvi.utils.attrdict method) topic_by_feature() (scvi.module.AmortizedLDAPyroModule method) TorchMRVAE (class in scvi.external.mrvi_torch) TorchMRVI (class in scvi.external) TOTALANVAE (class in scvi.external.totalanvi) TOTALANVI (class in scvi.external) 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.CYTOVI method) (scvi.external.Decipher method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.JaxMRVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.RESOLVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SCBASSET method) (scvi.external.SCVIVA method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.SysVI method) (scvi.external.Tangram method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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.SemisupervisedTrainingMixin method) (scvi.model.base.UnsupervisedTrainingMixin method) (scvi.model.CondSCVI method) (scvi.model.DestVI method) (scvi.model.JaxSCVI method) (scvi.model.LinearSCVI method) (scvi.model.mlxSCVI 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.MappedCollectionDataModule method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.dataloaders.TileDBDataModule method) (scvi.external.contrastivevi.ContrastiveDataSplitter method) train_indices (scvi.external.CellAssign attribute) (scvi.external.ContrastiveVI attribute) (scvi.external.CYTOVI attribute) (scvi.external.Decipher attribute) (scvi.external.DIAGVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JaxMRVI attribute) (scvi.external.METHYLANVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI attribute) (scvi.external.POISSONVI attribute) (scvi.external.RESOLVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SCBASSET attribute) (scvi.external.SCVIVA attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.SysVI attribute) (scvi.external.Tangram attribute) (scvi.external.TorchMRVI attribute) (scvi.external.TOTALANVI 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.mlxSCVI attribute) (scvi.model.MULTIVI attribute) (scvi.model.PEAKVI attribute) (scvi.model.SCANVI attribute) (scvi.model.SCVI attribute) (scvi.model.TOTALVI attribute) train_size (scvi.dataloaders.TileDBDataModule attribute) Trainer (class in scvi.train) TrainerConfig (class in scvi.train) training (scvi.external.cellassign.CellAssignModule attribute) (scvi.external.contrastivevi.ContrastiveVAE attribute) (scvi.external.cytovi.CytoVAE attribute) (scvi.external.decipher.DecipherPyroModule attribute) (scvi.external.diagvi.DIAGVAE attribute) (scvi.external.gimvi.JVAE attribute) (scvi.external.methylvi.METHYLANVAE attribute) (scvi.external.methylvi.METHYLVAE attribute) (scvi.external.mrvi.MRVAE attribute) (scvi.external.mrvi_jax.JaxMRVAE attribute) (scvi.external.mrvi_torch.TorchMRVAE attribute) (scvi.external.resolvi.RESOLVAE attribute) (scvi.external.scbasset.ScBassetModule attribute) (scvi.external.scviva.nicheVAE attribute) (scvi.external.stereoscope.RNADeconv attribute) (scvi.external.stereoscope.SpatialDeconv attribute) (scvi.external.sysvi.SysVAE attribute) (scvi.external.tangram.TangramMapper attribute) (scvi.external.totalanvi.TOTALANVAE 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.DecoderTOTALVI attribute) (scvi.nn.Embedding attribute) (scvi.nn.Encoder attribute) (scvi.nn.EncoderTOTALVI attribute) (scvi.nn.FCLayers attribute) (scvi.nn.LinearDecoderSCVI attribute) (scvi.train.AdversarialTrainingPlan attribute) (scvi.train.ClassifierTrainingPlan attribute) (scvi.train.JaxTrainingPlan attribute) (scvi.train.LowLevelPyroTrainingPlan attribute) (scvi.train.PyroTrainingPlan attribute) (scvi.train.SemiSupervisedAdversarialTrainingPlan 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.ClassifierTrainingPlan method) (scvi.train.JaxTrainingPlan method) (scvi.train.LowLevelPyroTrainingPlan method) (scvi.train.PyroTrainingPlan method) (scvi.train.SemiSupervisedAdversarialTrainingPlan method) (scvi.train.SemiSupervisedTrainingPlan method) (scvi.train.TrainingPlan method) TrainingPlan (class in scvi.train) TrainingPlanConfig (class in scvi.train) TrainRunner (class in scvi.train) Trajectory (class in scvi.external.decipher.utils) trajectory_latent (scvi.external.decipher.utils.Trajectory attribute) trajectory_time (scvi.external.decipher.utils.Trajectory attribute) transfer_batch_to_device() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.MappedCollectionDataModule method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.dataloaders.TileDBDataModule 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) (scvi.external.CellAssign method) (scvi.external.ContrastiveVI method) (scvi.external.CYTOVI method) (scvi.external.Decipher method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.JaxMRVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.RESOLVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SCBASSET method) (scvi.external.SCVIVA method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.SysVI method) (scvi.external.Tangram method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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.mlxSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI 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_jax.JaxMRVAE attribute) u_prior_mixture_k (scvi.external.mrvi_jax.JaxMRVAE attribute) u_prior_scale (scvi.external.mrvi_jax.JaxMRVAE attribute) UNLABELED_CATEGORY (scvi.data.fields.LabelsWithUnlabeledObsField attribute) unlabeled_category (scvi.dataloaders.MappedCollectionDataModule attribute) (scvi.dataloaders.TileDBDataModule attribute) unlock() (scvi.utils.attrdict method) unlocked() (scvi.utils.attrdict method) uns (scvi.dataloaders.CollectionAdapter attribute) UnsupervisedTrainingMixin (class in scvi.model.base) update() (scvi.utils.attrdict method) update_from_flattened_dict() (scvi.utils.attrdict method) update_only_decoder (scvi.train.TrainingPlanConfig attribute) update_sample_info() (scvi.external.JaxMRVI method) (scvi.external.TorchMRVI method) update_setup_method_args() (scvi.data.AnnDataManager method) (scvi.external.CellAssign method) (scvi.external.ContrastiveVI method) (scvi.external.CYTOVI method) (scvi.external.Decipher method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.JaxMRVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.RESOLVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SCBASSET method) (scvi.external.SCVIVA method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.SysVI method) (scvi.external.Tangram method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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.mlxSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI 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.MappedCollectionDataModule method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.dataloaders.TileDBDataModule method) (scvi.external.contrastivevi.ContrastiveDataSplitter 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) validate_sample() (scvi.distributions.JaxNegativeBinomialMeanDisp method) validation_indices (scvi.external.CellAssign attribute) (scvi.external.ContrastiveVI attribute) (scvi.external.CYTOVI attribute) (scvi.external.Decipher attribute) (scvi.external.DIAGVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JaxMRVI attribute) (scvi.external.METHYLANVI attribute) (scvi.external.METHYLVI attribute) (scvi.external.MRVI attribute) (scvi.external.POISSONVI attribute) (scvi.external.RESOLVI attribute) (scvi.external.RNAStereoscope attribute) (scvi.external.SCAR attribute) (scvi.external.SCBASSET attribute) (scvi.external.SCVIVA attribute) (scvi.external.SOLO attribute) (scvi.external.SpatialStereoscope attribute) (scvi.external.SysVI attribute) (scvi.external.Tangram attribute) (scvi.external.TorchMRVI attribute) (scvi.external.TOTALANVI 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.mlxSCVI attribute) (scvi.model.MULTIVI attribute) (scvi.model.PEAKVI attribute) (scvi.model.SCANVI attribute) (scvi.model.SCVI attribute) (scvi.model.TOTALVI attribute) validation_size (scvi.dataloaders.TileDBDataModule attribute) validation_step() (scvi.train.ClassifierTrainingPlan method) (scvi.train.JaxTrainingPlan method) (scvi.train.SemiSupervisedTrainingPlan method) (scvi.train.TrainingPlan method) values() (scvi.utils.attrdict method) var_names (scvi.dataloaders.MappedCollectionDataModule attribute) variance (scvi.distributions.BetaBinomial attribute) (scvi.distributions.JaxNegativeBinomialMeanDisp attribute) (scvi.distributions.Log1pNormal attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.Normal attribute) (scvi.distributions.Poisson attribute) (scvi.distributions.ZeroInflatedGamma attribute) (scvi.distributions.ZeroInflatedLogNormal 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.CYTOVI method) (scvi.external.Decipher method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.JaxMRVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.RESOLVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SCBASSET method) (scvi.external.SCVIVA method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.SysVI method) (scvi.external.Tangram method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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.mlxSCVI 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) (scvi.external.CellAssign method) (scvi.external.ContrastiveVI method) (scvi.external.CYTOVI method) (scvi.external.Decipher method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.JaxMRVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.RESOLVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SCBASSET method) (scvi.external.SCVIVA method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.SysVI method) (scvi.external.Tangram method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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.mlxSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI method) view_setup_args() (scvi.external.CellAssign static method) (scvi.external.ContrastiveVI static method) (scvi.external.CYTOVI static method) (scvi.external.Decipher static method) (scvi.external.DIAGVI static method) (scvi.external.GIMVI static method) (scvi.external.JaxMRVI static method) (scvi.external.METHYLANVI static method) (scvi.external.METHYLVI static method) (scvi.external.MRVI static method) (scvi.external.POISSONVI static method) (scvi.external.RESOLVI static method) (scvi.external.RNAStereoscope static method) (scvi.external.SCAR static method) (scvi.external.SCBASSET static method) (scvi.external.SCVIVA static method) (scvi.external.SOLO static method) (scvi.external.SpatialStereoscope static method) (scvi.external.SysVI static method) (scvi.external.Tangram static method) (scvi.external.TorchMRVI static method) (scvi.external.TOTALANVI 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.mlxSCVI 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) (scvi.external.CellAssign method) (scvi.external.ContrastiveVI method) (scvi.external.CYTOVI method) (scvi.external.Decipher method) (scvi.external.DIAGVI method) (scvi.external.GIMVI method) (scvi.external.JaxMRVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.RESOLVI method) (scvi.external.RNAStereoscope method) (scvi.external.SCAR method) (scvi.external.SCBASSET method) (scvi.external.SCVIVA method) (scvi.external.SOLO method) (scvi.external.SpatialStereoscope method) (scvi.external.SysVI method) (scvi.external.Tangram method) (scvi.external.TorchMRVI method) (scvi.external.TOTALANVI 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.mlxSCVI method) (scvi.model.MULTIVI method) (scvi.model.PEAKVI method) (scvi.model.SCANVI method) (scvi.model.SCVI method) (scvi.model.TOTALVI 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) weight_decay (scvi.train.AdversarialTrainingPlanConfig attribute) (scvi.train.ClassifierTrainingPlanConfig attribute) (scvi.train.JaxTrainingPlanConfig attribute) (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig attribute) Z z_u_prior (scvi.external.mrvi_jax.JaxMRVAE attribute) z_u_prior_scale (scvi.external.mrvi_jax.JaxMRVAE attribute) zero_fraction() (scvi.criticism.PosteriorPredictiveCheck method) ZeroInflatedGamma (class in scvi.distributions) ZeroInflatedLogNormal (class in scvi.distributions) ZeroInflatedNegativeBinomial (class in scvi.distributions) zi_logits (scvi.distributions.ZeroInflatedGamma attribute) (scvi.distributions.ZeroInflatedLogNormal attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) zi_probs (scvi.distributions.ZeroInflatedGamma attribute) (scvi.distributions.ZeroInflatedLogNormal attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute)
