Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | Z A 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.DRVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI attribute) (scvi.external.VELOVI attribute) (scvi.external.VIVS 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.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.DRVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI attribute) (scvi.external.VELOVI attribute) (scvi.external.VIVS 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.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) AmortizedLDA (class in scvi.model) AmortizedLDAPyroModule (class in scvi.module) AnnbatchDataModule (class in scvi.dataloaders) anndata_version (scvi.hub.HubMetadata attribute) (scvi.hub.HubModelCardHelper attribute) AnnDataLoader (class in scvi.dataloaders) AnnDataManager (class in scvi.data) AnnDataManagerValidationCheck (class in scvi.data) AnnTorchDataset (class in scvi.data) ArchesMixin (class in scvi.model.base) arg_constraints (scvi.distributions.BetaBinomial attribute) (scvi.distributions.Log1pNormal attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.ZeroInflatedGamma attribute) (scvi.distributions.ZeroInflatedLogNormal attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) (scvi.external.drvi.LogNegativeBinomial attribute) 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.external.decipher._trainingplan.DecipherTrainingPlan 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.AnnbatchDataModule attribute) (scvi.dataloaders.MappedCollectionDataModule attribute) batch_size (scvi._settings.ScviConfig attribute) (scvi.dataloaders.AnnDataLoader attribute) (scvi.dataloaders.ConcatDataLoader attribute) (scvi.dataloaders.SemiSupervisedDataLoader attribute) (scvi.external.contrastivevi.ContrastiveDataLoader attribute) (scvi.external.gimvi._task.CyclicMultiDataLoader attribute) BatchDistributedSampler (class in scvi.dataloaders) benchmark (scvi.train.TrainerConfig attribute) BetaBinomial (class in scvi.distributions) bias (scvi.external.drvi.StackedLinearLayer attribute) blocked (scvi.train.PyroTrainingPlanConfig attribute) brainlarge_dataset() (in module scvi.data) breast_cancer_dataset() (in module scvi.data) BSSeqMixin (class in scvi.external.methylvi) BSSeqModuleMixin (class in scvi.external.methylvi) C calculate_interpretability_scores() (scvi.external.DRVI method) 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) 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) 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) 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() (scvi.train._metrics.ElboMetric method) 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) compute_imputed_gene_expression() (scvi.external.Decipher method) compute_local_statistics() (scvi.external.MRVI method) ConcatDataLoader (class in scvi.dataloaders) CondSCVI (class in scvi.model) configure_optimizers() (scvi.external.decipher._trainingplan.DecipherTrainingPlan method) (scvi.train.AdversarialTrainingPlan method) (scvi.train.ClassifierTrainingPlan method) (scvi.train.LowLevelPyroTrainingPlan method) (scvi.train.PyroTrainingPlan method) (scvi.train.SemiSupervisedAdversarialTrainingPlan method) (scvi.train.TrainingPlan method) confusion_coarse_celltypes() (scvi.model.CondSCVI method) construct_custom_guidance_graph() (scvi.external.DIAGVI static method) ContrastiveDataLoader (class in scvi.external.contrastivevi) ContrastiveDataSplitter (class in scvi.external.contrastivevi) ContrastiveVAE (class in scvi.external.contrastivevi) ContrastiveVI (class in scvi.external) 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.DRVI class method) (scvi.external.GIMVI class method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI class method) (scvi.external.VELOVI class method) (scvi.external.VIVS 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.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) cortex() (in module scvi.data) create_criticism_report() (in module scvi.criticism) 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) CyclicMultiDataLoader (class in scvi.external.gimvi._task) CytoVAE (class in scvi.external.cytovi) CYTOVI (class in scvi.external) D data (scvi.autotune.AutotuneExperiment attribute) (scvi.data.AnnTorchDataset attribute) data_input_keys (scvi.external.methylvi.BSSeqModuleMixin 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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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.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) (scvi.external.contrastivevi.ContrastiveDataLoader attribute) (scvi.external.gimvi._task.CyclicMultiDataLoader attribute) dataset_10x() (in module scvi.data) DataSplitter (class in scvi.dataloaders) Decipher (class in scvi.external) DecipherPyroModule (class in scvi.external.decipher) DecipherTrainingPlan (class in scvi.external.decipher._trainingplan) Decoder (class in scvi.nn) DecoderDRVI (class in scvi.external.drvi) DecoderMETHYLVI (class in scvi.external.methylvi) 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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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.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.DRVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI attribute) (scvi.external.VELOVI attribute) (scvi.external.VIVS 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.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) 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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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.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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI 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.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) (scvi.external.methylvi.BSSeqMixin method) differential_niche_abundance() (scvi.external.RESOLVI method) DifferentialComputation (class in scvi.model.base) DifferentialExpressionResults (class in scvi.external.scviva.differential_expression) 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) (scvi.external.contrastivevi.ContrastiveDataLoader attribute) (scvi.external.gimvi._task.CyclicMultiDataLoader attribute) DRVI (class in scvi.external) DRVIModule (class in scvi.external.drvi) 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) ElboMetric (class in scvi.train._metrics) 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) EncoderTOTALVI (class in scvi.nn) eps (scvi.train.ClassifierTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig attribute) experiment_name (scvi.autotune.AutotuneExperiment attribute) extend() (scvi.nn.Embedding class method) extra_categorical_covs (scvi.dataloaders.AnnbatchDataModule attribute) (scvi.dataloaders.MappedCollectionDataModule attribute) (scvi.dataloaders.TileDBDataModule attribute) extra_continuous_covs (scvi.dataloaders.AnnbatchDataModule attribute) (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) extra_repr() (scvi.external.drvi.StackedLinearLayer method) 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) fn() (scvi.external.mrvi._types.MRVIReduction method) forward() (scvi.external.drvi.DecoderDRVI method) (scvi.external.drvi.StackedLinearLayer method) (scvi.external.methylvi.DecoderMETHYLVI method) (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.nn.MultiDecoder method) (scvi.nn.MultiEncoder method) (scvi.train.ClassifierTrainingPlan method) (scvi.train.LowLevelPyroTrainingPlan method) (scvi.train.TrainingPlan method) freeze (scvi.nn.Embedding attribute) 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) full_state_update (scvi.train._metrics.ElboMetric attribute) G g1_g2 (scvi.external.scviva.differential_expression.DifferentialExpressionResults attribute) g1_n1 (scvi.external.scviva.differential_expression.DifferentialExpressionResults attribute) generative() (scvi.external.cellassign.CellAssignModule method) (scvi.external.contrastivevi.ContrastiveVAE method) (scvi.external.cytovi.CytoVAE method) (scvi.external.diagvi.DIAGVAE method) (scvi.external.drvi.DRVIModule method) (scvi.external.gimvi.JVAE method) (scvi.external.methylvi.METHYLVAE method) (scvi.external.mrvi.MRVAE 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.MRDeconv method) (scvi.module.MULTIVAE method) (scvi.module.PEAKVAE method) (scvi.module.TOTALVAE method) (scvi.module.VAE method) (scvi.module.VAEC method) get_aggregated_posterior() (scvi.external.CYTOVI method) (scvi.external.DIAGVI method) (scvi.external.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.SCVIVA method) (scvi.external.SysVI method) (scvi.external.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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 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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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.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_batch_representation() (scvi.external.DRVI method) (scvi.external.JointEmbeddingSCVI method) (scvi.external.MRVI method) (scvi.external.SCVIVA 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_cell_scores() (scvi.external.VIVS 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_effect_of_splits_out_of_distribution() (scvi.external.DRVI method) get_effect_of_splits_within_distribution() (scvi.external.DRVI method) get_elbo() (scvi.external.CYTOVI method) (scvi.external.DIAGVI method) (scvi.external.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.SCVIVA method) (scvi.external.SysVI method) (scvi.external.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.SCVIVA method) (scvi.external.SysVI 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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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.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_correlations() (scvi.external.VIVS method) get_gene_groupings() (scvi.external.VIVS method) get_gene_likelihood() (scvi.external.VELOVI method) get_hier_importance() (scvi.external.VIVS method) get_importance() (scvi.external.VIVS method) get_importance_weights() (scvi.external.CellAssign method) (scvi.external.CYTOVI method) (scvi.external.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.SCVIVA method) (scvi.external.SysVI 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_interpretability_scores() (scvi.external.DRVI method) get_intervals_recorded() (scvi.train._metrics.ElboMetric method) get_latent_library_size() (scvi.external.CellAssign method) (scvi.external.ContrastiveVI method) (scvi.external.CYTOVI method) (scvi.external.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.SCVIVA method) (scvi.external.SysVI 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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI 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.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS method) (scvi.model.AmortizedLDA method) (scvi.model.AUTOZI method) (scvi.model.base.VAEMixin method) (scvi.model.CondSCVI method) (scvi.model.DestVI 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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.SCVIVA method) (scvi.external.SysVI 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.MRVI method) get_local_sample_representation() (scvi.external.MRVI method) get_logger() (scvi.autotune.AutotuneExperiment method) get_mapper_matrix() (scvi.external.Tangram method) get_marginal_ll() (scvi.external.CYTOVI method) (scvi.external.DIAGVI method) (scvi.external.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.SCVIVA method) (scvi.external.SysVI method) (scvi.external.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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.external.drvi.LogNegativeBinomial 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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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.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.DRVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI attribute) (scvi.external.VELOVI attribute) (scvi.external.VIVS 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.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) (scvi.external.methylvi.BSSeqMixin method) get_optimizer_creator() (scvi.train.TrainingPlan method) get_outlier_cell_sample_pairs() (scvi.external.MRVI method) get_params() (scvi.external.stereoscope.RNADeconv method) get_permutation_scores() (scvi.external.VELOVI method) get_perplexity() (scvi.model.AmortizedLDA method) get_proportions() (scvi.external.SpatialStereoscope method) (scvi.external.stereoscope.SpatialDeconv method) (scvi.model.DestVI method) 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_effect_of_each_split() (scvi.external.DRVI method) get_reconstruction_error() (scvi.external.CYTOVI method) (scvi.external.DIAGVI method) (scvi.external.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI method) (scvi.external.METHYLANVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.SCVIVA method) (scvi.external.SysVI method) (scvi.external.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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_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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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.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) (scvi.external.methylvi.BSSeqMixin 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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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.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_tuner() (scvi.autotune.AutotuneExperiment 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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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.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) GIMVITrainingPlan (class in scvi.external.gimvi._task) gpc (scvi.external.scviva.differential_expression.DifferentialExpressionResults attribute) gpc_info() (scvi.external.scviva.differential_expression.DifferentialExpressionResults method) group_by (scvi.external.mrvi._types.MRVIReduction attribute) 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 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.DRVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI attribute) (scvi.external.VELOVI attribute) (scvi.external.VIVS 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.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) HubMetadata (class in scvi.hub) HubModel (class in scvi.hub) HubModelCardHelper (class in scvi.hub) I id (scvi.autotune.AutotuneExperiment attribute) impute_categories_from_reference() (scvi.external.CYTOVI method) impute_rna_from_reference() (scvi.external.CYTOVI method) in_features (scvi.external.drvi.StackedLinearLayer attribute) 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.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.MRDeconv method) (scvi.module.MULTIVAE method) (scvi.module.PEAKVAE method) (scvi.module.VAEC method) inference_dataloader() (scvi.dataloaders.AnnbatchDataModule method) (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) input (scvi.external.mrvi._types.MRVIReduction attribute) interval (scvi.train._metrics.ElboMetric 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_trained (scvi.external.CellAssign attribute) (scvi.external.ContrastiveVI attribute) (scvi.external.CYTOVI attribute) (scvi.external.Decipher attribute) (scvi.external.DIAGVI attribute) (scvi.external.DRVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI attribute) (scvi.external.VELOVI attribute) (scvi.external.VIVS 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.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_view (scvi.dataloaders.CollectionAdapter attribute) isbacked (scvi.dataloaders.CollectionAdapter attribute) iterate_on_ae_output() (scvi.external.DRVI method) iterate_on_decoded_latent_samples() (scvi.external.DRVI method) iterate_on_effect_of_splits_within_distribution() (scvi.external.DRVI method) J JointEmbeddingSCVI (class in scvi.external) JointEmbeddingVAE (class in scvi.external) JVAE (class in scvi.external.gimvi) K key_adversarial (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) keys_and_dtypes (scvi.data.AnnTorchDataset attribute) kl_global (scvi.module.base.LossOutput attribute) kl_global_sum (scvi.module.base.LossOutput attribute) kl_local (scvi.module.base.LossOutput attribute) kl_local_sum (scvi.module.base.LossOutput attribute) kl_weight (scvi.train.LowLevelPyroTrainingPlan attribute) (scvi.train.TrainingPlan attribute) KwargsConfig (class in scvi.train) L label_keys (scvi.dataloaders.MappedCollectionDataModule attribute) labels (scvi.dataloaders.MappedCollectionDataModule attribute) labels_key (scvi.train.ClassifierTrainingPlanConfig attribute) labels_mapping (scvi.dataloaders.AnnbatchDataModule attribute) (scvi.dataloaders.TileDBDataModule attribute) LabelsWithUnlabeledObsField (class in scvi.data.fields) 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) 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.DRVI class method) (scvi.external.GIMVI class method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI class method) (scvi.external.VELOVI class method) (scvi.external.VIVS 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.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_model() (scvi.hub.HubModel method) load_query_data() (scvi.external.CYTOVI class method) (scvi.external.DRVI class method) (scvi.external.JointEmbeddingSCVI 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.SCVIVA class method) (scvi.external.SysVI 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.DRVI static method) (scvi.external.GIMVI static method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI static method) (scvi.external.VELOVI static method) (scvi.external.VIVS 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.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.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) local_dir (scvi.hub.HubModel attribute) Log1pNormal (class in scvi.distributions) log_every_n_steps (scvi.train.TrainerConfig attribute) log_prob() (scvi.distributions.Log1pNormal method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture method) (scvi.distributions.ZeroInflatedGamma method) (scvi.distributions.ZeroInflatedLogNormal method) (scvi.distributions.ZeroInflatedNegativeBinomial method) (scvi.external.drvi.LogNegativeBinomial 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) (scvi.autotune.AutotuneExperiment attribute) logits (scvi.module.base.LossOutput attribute) LogNegativeBinomial (class in scvi.external.drvi) 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.JointEmbeddingVAE method) (scvi.external.methylvi.METHYLANVAE method) (scvi.external.methylvi.METHYLVAE method) (scvi.external.mrvi.MRVAE 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.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.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.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) max_epochs (scvi.train.TrainerConfig attribute) max_kl_weight (scvi.train.TrainingPlanConfig attribute) max_norm (scvi.nn.Embedding attribute) mean (scvi.distributions.Log1pNormal attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.ZeroInflatedGamma attribute) (scvi.distributions.ZeroInflatedLogNormal attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) (scvi.external.drvi.LogNegativeBinomial 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 (scvi.autotune.AutotuneExperiment attribute) metrics_callback (scvi.autotune.AutotuneExperiment attribute) metrics_report (scvi.hub.HubModelCardHelper attribute) min_kl_weight (scvi.train.TrainingPlanConfig attribute) minified_data_type (scvi.external.DRVI attribute) (scvi.external.JointEmbeddingSCVI attribute) (scvi.external.MRVI attribute) (scvi.external.SCVIVA 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.DRVI method) (scvi.external.JointEmbeddingSCVI method) (scvi.external.MRVI method) (scvi.external.SCVIVA 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.autotune.AutotuneExperiment attribute) (scvi.train._metrics.ElboMetric 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 (scvi.autotune.AutotuneExperiment 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 (class in scvi.external.mrvi) MRVI (class in scvi.external) MRVIReduction (class in scvi.external.mrvi._types) mu (scvi.external.drvi.LogNegativeBinomial attribute) 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) MultiDecoder (class in scvi.nn) MultiEncoder (class in scvi.nn) MULTIVAE (class in scvi.module) MULTIVI (class in scvi.model) N n1_g2 (scvi.external.scviva.differential_expression.DifferentialExpressionResults attribute) n1_index (scvi.external.scviva.differential_expression.DifferentialExpressionResults attribute) n1_n2 (scvi.external.scviva.differential_expression.DifferentialExpressionResults attribute) n2_index (scvi.external.scviva.differential_expression.DifferentialExpressionResults attribute) n_batch (scvi.dataloaders.AnnbatchDataModule attribute) (scvi.dataloaders.MappedCollectionDataModule attribute) (scvi.dataloaders.TileDBDataModule attribute) N_CATS_PER_KEY (scvi.data.fields.CategoricalJointObsField attribute) (scvi.data.fields.CategoricalJointVarField attribute) N_CELLS_KEY (scvi.data.fields.LayerField attribute) n_epochs_kl_warmup (scvi.train.AdversarialTrainingPlanConfig attribute) (scvi.train.LowLevelPyroTrainingPlanConfig attribute) (scvi.train.PyroTrainingPlanConfig attribute) (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig attribute) n_labels (scvi.dataloaders.AnnbatchDataModule attribute) (scvi.dataloaders.MappedCollectionDataModule attribute) (scvi.dataloaders.TileDBDataModule attribute) n_obs (scvi.dataloaders.AnnbatchDataModule attribute) (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.dataloaders.AnnbatchDataModule 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_samples (scvi.dataloaders.AnnbatchDataModule attribute) (scvi.dataloaders.MappedCollectionDataModule attribute) (scvi.dataloaders.TileDBDataModule attribute) n_stacks (scvi.external.drvi.StackedLinearLayer attribute) n_steps_kl_warmup (scvi.train.AdversarialTrainingPlanConfig 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.AnnbatchDataModule attribute) (scvi.dataloaders.MappedCollectionDataModule attribute) (scvi.dataloaders.TileDBDataModule attribute) N_VARS_KEY (scvi.data.fields.LayerField attribute) name (scvi.external.mrvi._types.MRVIReduction attribute) (scvi.train._metrics.ElboMetric 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_samples (scvi.autotune.AutotuneExperiment 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) (scvi.external.contrastivevi.ContrastiveDataLoader attribute) (scvi.external.gimvi._task.CyclicMultiDataLoader 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) on_before_backward() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) on_before_batch_transfer() (scvi.dataloaders.AnnbatchDataModule method) (scvi.dataloaders.MappedCollectionDataModule 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.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.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) (scvi.train.TrainingPlan method) on_train_epoch_end() (scvi.external.decipher._trainingplan.DecipherTrainingPlan method) (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.external.decipher._trainingplan.DecipherTrainingPlan method) (scvi.external.gimvi._task.GIMVITrainingPlan method) (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_model_train() (scvi.external.decipher._trainingplan.DecipherTrainingPlan 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.SemiSupervisedAdversarialTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig attribute) optimizer_creator (scvi.train.AdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig attribute) optimizer_step() (scvi.external.decipher._trainingplan.DecipherTrainingPlan 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) out_features (scvi.external.drvi.StackedLinearLayer attribute) P padding_idx (scvi.nn.Embedding 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) pin_memory (scvi.dataloaders.AnnDataLoader attribute) (scvi.dataloaders.ConcatDataLoader attribute) (scvi.dataloaders.SemiSupervisedDataLoader attribute) (scvi.external.contrastivevi.ContrastiveDataLoader attribute) (scvi.external.gimvi._task.CyclicMultiDataLoader attribute) pin_memory_device (scvi.dataloaders.AnnDataLoader attribute) (scvi.dataloaders.ConcatDataLoader attribute) (scvi.dataloaders.SemiSupervisedDataLoader attribute) (scvi.external.contrastivevi.ContrastiveDataLoader attribute) (scvi.external.gimvi._task.CyclicMultiDataLoader attribute) plot() (scvi.external.scviva.differential_expression.DifferentialExpressionResults method) 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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI method) (scvi.external.METHYLVI method) (scvi.external.MRVI method) (scvi.external.POISSONVI method) (scvi.external.SCAR method) (scvi.external.SCVIVA method) (scvi.external.SysVI 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_neighborhood() (scvi.external.SCVIVA method) predict_niche_activation() (scvi.external.SCVIVA method) predict_t() (scvi.external.VIVS method) predictive_log_likelihood() (scvi.external.decipher.DecipherPyroModule method) prefetch_factor (scvi.dataloaders.AnnDataLoader attribute) (scvi.dataloaders.ConcatDataLoader attribute) (scvi.dataloaders.SemiSupervisedDataLoader attribute) (scvi.external.contrastivevi.ContrastiveDataLoader attribute) (scvi.external.gimvi._task.CyclicMultiDataLoader attribute) prefrontalcortex_starmap() (in module scvi.data) prepare_query_anndata() (scvi.external.CYTOVI static method) (scvi.external.DRVI static method) (scvi.external.JointEmbeddingSCVI 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.SCVIVA static method) (scvi.external.SysVI 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.DRVI static method) (scvi.external.JointEmbeddingSCVI 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.SCVIVA static method) (scvi.external.SysVI 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) 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) 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.DRVI class method) (scvi.external.GIMVI class method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI class method) (scvi.external.VELOVI class method) (scvi.external.VIVS 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.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) registry (scvi.data.AnnDataManager attribute) (scvi.dataloaders.AnnbatchDataModule 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.DRVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI attribute) (scvi.external.VELOVI attribute) (scvi.external.VIVS 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.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) reparameterize_transformation() (scvi.nn.EncoderTOTALVI method) repo_name (scvi.hub.HubModel attribute) required (scvi.data.fields.CategoricalJointObsField attribute) (scvi.data.fields.CategoricalJointVarField attribute) (scvi.data.fields.NumericalJointObsField attribute) (scvi.data.fields.NumericalJointVarField attribute) resample_labels() (scvi.dataloaders.SemiSupervisedDataLoader method) rescale_dropout() (scvi.module.AutoZIVAE method) reset_logging_handler() (scvi._settings.ScviConfig method) reset_parameters() (scvi.external.drvi.StackedLinearLayer method) reshape_bernoulli() (scvi.module.AutoZIVAE method) RESOLVAE (class in scvi.external.resolvi) RESOLVI (class in scvi.external) resources (scvi.autotune.AutotuneExperiment attribute) result_grid (scvi.autotune.AutotuneExperiment attribute) retina() (in module scvi.data) RNADeconv (class in scvi.external.stereoscope) RNASeqMixin (class in scvi.model.base) RNAStereoscope (class in scvi.external) 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.DRVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI attribute) (scvi.external.VELOVI attribute) (scvi.external.VIVS 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.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.DRVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI attribute) (scvi.external.VELOVI attribute) (scvi.external.VIVS 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.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) S sample() (scvi.distributions.BetaBinomial method) (scvi.distributions.Log1pNormal method) (scvi.distributions.NegativeBinomial method) (scvi.distributions.NegativeBinomialMixture 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.drvi.LogNegativeBinomial method) (scvi.external.methylvi.METHYLVAE 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.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_posterior() (scvi.external.RESOLVI method) (scvi.model.base.PyroSampleMixin method) sample_rate() (scvi.external.gimvi.JVAE method) sample_scale() (scvi.external.gimvi.JVAE method) sampler (scvi.dataloaders.AnnDataLoader attribute) (scvi.dataloaders.ConcatDataLoader attribute) (scvi.dataloaders.SemiSupervisedDataLoader attribute) (scvi.external.contrastivevi.ContrastiveDataLoader attribute) (scvi.external.gimvi._task.CyclicMultiDataLoader attribute) samples (scvi.dataloaders.MappedCollectionDataModule attribute) samples_mapping (scvi.dataloaders.AnnbatchDataModule attribute) (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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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.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) SaveCheckpoint (class in scvi.train) scale (scvi.external.drvi.LogNegativeBinomial 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_sampler() (scvi.model.base.DifferentialComputation method) SCANVAE (class in scvi.module) SCANVI (class in scvi.model) SCAR (class in scvi.external) SCBASSET (class in scvi.external) ScBassetModule (class in scvi.external.scbasset) scheduler (scvi.autotune.AutotuneExperiment attribute) scheduler_kwargs (scvi.autotune.AutotuneExperiment attribute) scib_metrics_callback (scvi.autotune.AutotuneExperiment attribute) ScibCallback (class in scvi.train) 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) search_space (scvi.autotune.AutotuneExperiment attribute) searcher (scvi.autotune.AutotuneExperiment attribute) searcher_kwargs (scvi.autotune.AutotuneExperiment attribute) seed (scvi._settings.ScviConfig attribute) (scvi.autotune.AutotuneExperiment attribute) 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_batch_size() (scvi.dataloaders.AnnbatchDataModule method) set_latent_dimension_stats() (scvi.external.DRVI method) set_online_update_hooks() (scvi.nn.FCLayers method) set_split() (scvi.dataloaders.AnnbatchDataModule method) setup() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter method) (scvi.dataloaders.TileDBDataModule method) (scvi.external.contrastivevi.ContrastiveDataSplitter method) (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) setup_annbatch() (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.DRVI class method) (scvi.external.GIMVI class method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI class method) (scvi.external.VELOVI class method) (scvi.external.VIVS 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.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() (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.DRVI class method) (scvi.external.GIMVI class method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI class method) (scvi.external.VELOVI class method) (scvi.external.VIVS 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.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_method_args (scvi.autotune.AutotuneExperiment attribute) setup_method_name (scvi.autotune.AutotuneExperiment attribute) 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) 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) SplitFCLayers (class in scvi.external.drvi) StackedLinearLayer (class in scvi.external.drvi) state_dict() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) state_key (scvi.model.base.PyroJitGuideWarmup attribute) (scvi.model.base.PyroModelGuideWarmup 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.DRVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI attribute) (scvi.external.VELOVI attribute) (scvi.external.VIVS 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.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.Log1pNormal attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.NegativeBinomialMixture attribute) (scvi.distributions.ZeroInflatedGamma attribute) (scvi.distributions.ZeroInflatedLogNormal attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) (scvi.external.drvi.LogNegativeBinomial 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) teardown() (scvi.model.base.PyroJitGuideWarmup method) (scvi.model.base.PyroModelGuideWarmup method) (scvi.train.LoudEarlyStopping method) test_dataloader() (scvi.dataloaders.DataSplitter method) (scvi.dataloaders.SemiSupervisedDataSplitter 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.DRVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI attribute) (scvi.external.VELOVI attribute) (scvi.external.VIVS 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.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) theta (scvi.external.drvi.LogNegativeBinomial attribute) TileDBDataModule (class in scvi.dataloaders) timeout (scvi.dataloaders.AnnDataLoader attribute) (scvi.dataloaders.ConcatDataLoader attribute) (scvi.dataloaders.SemiSupervisedDataLoader attribute) (scvi.external.contrastivevi.ContrastiveDataLoader attribute) (scvi.external.gimvi._task.CyclicMultiDataLoader attribute) tissues (scvi.hub.HubModelCardHelper attribute) to_device() (scvi.external.CellAssign method) (scvi.external.ContrastiveVI method) (scvi.external.CYTOVI method) (scvi.external.Decipher method) (scvi.external.DIAGVI method) (scvi.external.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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.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) to_kwargs() (scvi.train.AdversarialTrainingPlanConfig method) (scvi.train.ClassifierTrainingPlanConfig method) (scvi.train.KwargsConfig 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) topic_by_feature() (scvi.module.AmortizedLDAPyroModule method) 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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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.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) train_dataloader() (scvi.dataloaders.AnnbatchDataModule method) (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.DRVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI attribute) (scvi.external.VELOVI attribute) (scvi.external.VIVS 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.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.AnnbatchDataModule attribute) (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._trainingplan.DecipherTrainingPlan attribute) (scvi.external.decipher.DecipherPyroModule attribute) (scvi.external.diagvi.DIAGVAE attribute) (scvi.external.drvi.DecoderDRVI attribute) (scvi.external.drvi.DRVIModule attribute) (scvi.external.drvi.SplitFCLayers attribute) (scvi.external.drvi.StackedLinearLayer attribute) (scvi.external.gimvi._task.GIMVITrainingPlan attribute) (scvi.external.gimvi.JVAE attribute) (scvi.external.JointEmbeddingVAE attribute) (scvi.external.methylvi.DecoderMETHYLVI attribute) (scvi.external.methylvi.METHYLANVAE attribute) (scvi.external.methylvi.METHYLVAE attribute) (scvi.external.mrvi.MRVAE 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.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.nn.MultiDecoder attribute) (scvi.nn.MultiEncoder attribute) (scvi.train._metrics.ElboMetric attribute) (scvi.train.AdversarialTrainingPlan attribute) (scvi.train.ClassifierTrainingPlan 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.external.decipher._trainingplan.DecipherTrainingPlan method) (scvi.external.gimvi._task.GIMVITrainingPlan method) (scvi.train.AdversarialTrainingPlan method) (scvi.train.ClassifierTrainingPlan 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) 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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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.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) true_labels (scvi.module.base.LossOutput attribute) U UNLABELED_CATEGORY (scvi.data.fields.LabelsWithUnlabeledObsField attribute) unlabeled_category (scvi.dataloaders.AnnbatchDataModule attribute) (scvi.dataloaders.MappedCollectionDataModule attribute) (scvi.dataloaders.TileDBDataModule attribute) uns (scvi.dataloaders.CollectionAdapter attribute) UnsupervisedTrainingMixin (class in scvi.model.base) update() (scvi.train._metrics.ElboMetric method) update_only_decoder (scvi.train.TrainingPlanConfig attribute) update_sample_info() (scvi.external.MRVI 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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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.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.AnnbatchDataModule method) (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_field() (scvi.data.fields.BaseAnnDataField method) (scvi.data.fields.BaseMuDataWrapperClass method) (scvi.data.fields.CategoricalJointObsField method) (scvi.data.fields.CategoricalJointVarField method) (scvi.data.fields.CategoricalObsField method) (scvi.data.fields.CategoricalVarField method) (scvi.data.fields.LabelsWithUnlabeledObsField method) (scvi.data.fields.LayerField method) (scvi.data.fields.MuDataCategoricalJointObsField method) (scvi.data.fields.MuDataCategoricalJointVarField method) (scvi.data.fields.MuDataCategoricalObsField method) (scvi.data.fields.MuDataCategoricalVarField method) (scvi.data.fields.MuDataLayerField method) (scvi.data.fields.MuDataNumericalJointObsField method) (scvi.data.fields.MuDataNumericalJointVarField method) (scvi.data.fields.MuDataNumericalObsField method) (scvi.data.fields.MuDataNumericalVarField method) (scvi.data.fields.MuDataObsmField method) (scvi.data.fields.MuDataProteinLayerField method) (scvi.data.fields.MuDataVarmField method) (scvi.data.fields.NumericalJointObsField method) (scvi.data.fields.NumericalJointVarField method) (scvi.data.fields.ObsmField method) (scvi.data.fields.ProteinObsmField method) (scvi.data.fields.StringUnsField method) (scvi.data.fields.VarmField method) validation_indices (scvi.external.CellAssign attribute) (scvi.external.ContrastiveVI attribute) (scvi.external.CYTOVI attribute) (scvi.external.Decipher attribute) (scvi.external.DIAGVI attribute) (scvi.external.DRVI attribute) (scvi.external.GIMVI attribute) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI attribute) (scvi.external.VELOVI attribute) (scvi.external.VIVS 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.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.external.decipher._trainingplan.DecipherTrainingPlan method) (scvi.external.gimvi._task.GIMVITrainingPlan method) (scvi.train.ClassifierTrainingPlan method) (scvi.train.SemiSupervisedTrainingPlan method) (scvi.train.TrainingPlan method) var_names (scvi.dataloaders.MappedCollectionDataModule attribute) variance (scvi.distributions.Log1pNormal attribute) (scvi.distributions.NegativeBinomial attribute) (scvi.distributions.ZeroInflatedGamma attribute) (scvi.distributions.ZeroInflatedLogNormal attribute) (scvi.distributions.ZeroInflatedNegativeBinomial attribute) (scvi.external.drvi.LogNegativeBinomial 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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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.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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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.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.DRVI static method) (scvi.external.GIMVI static method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI static method) (scvi.external.VELOVI static method) (scvi.external.VIVS 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.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.DRVI method) (scvi.external.GIMVI method) (scvi.external.JointEmbeddingSCVI 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.TOTALANVI method) (scvi.external.VELOVI method) (scvi.external.VIVS 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.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) VIVS (class in scvi.external) W warnings_stacklevel (scvi._settings.ScviConfig attribute) weight (scvi.external.drvi.StackedLinearLayer attribute) (scvi.nn.Embedding attribute) weight_decay (scvi.train.AdversarialTrainingPlanConfig attribute) (scvi.train.ClassifierTrainingPlanConfig attribute) (scvi.train.SemiSupervisedAdversarialTrainingPlanConfig attribute) (scvi.train.SemiSupervisedTrainingPlanConfig attribute) (scvi.train.TrainingPlanConfig attribute) Z 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)
