Index A | B | C | D | E | F | G | H | I | L | M | N | P | R | S | T | V | W A adapt_annotation() (in module scdlkit) adapt_scgpt_annotation() (in module scdlkit.foundation) AdapterConfig (class in scdlkit.foundation) annotate_adata() (scdlkit.AnnotationRunner method) (scdlkit.foundation.ScGPTAnnotationRunner method) AnnotationRunner (class in scdlkit) AutoEncoder (class in scdlkit.models.autoencoder) B batch_size (scdlkit.foundation.ScGPTPreparedData attribute) (scdlkit.foundation.ScGPTSplitData attribute) C checkpoint_id (scdlkit.foundation.ScGPTAnnotationDataReport attribute) (scdlkit.foundation.ScGPTPreparedData attribute) (scdlkit.foundation.ScGPTSplitData attribute) class_counts (scdlkit.foundation.ScGPTAnnotationDataReport attribute) ClassificationModuleAdapter (class in scdlkit.adapters) compare_models() (in module scdlkit) compute_task_loss() (scdlkit.foundation.ScGPTAnnotationModel method) create_model() (in module scdlkit.models.registry) D dataset (scdlkit.foundation.ScGPTPreparedData attribute) DenoisingAutoEncoder (class in scdlkit.models.denoising) E encode() (scdlkit.runner.TaskRunner method) ensure_scgpt_checkpoint() (in module scdlkit.foundation) evaluate() (scdlkit.runner.TaskRunner method) evaluate_predictions() (in module scdlkit.evaluation) F fit() (scdlkit.runner.TaskRunner method) (scdlkit.training.trainer.Trainer method) fit_compare() (scdlkit.AnnotationRunner method) (scdlkit.foundation.ScGPTAnnotationRunner method) forward() (scdlkit.adapters.ClassificationModuleAdapter method) (scdlkit.adapters.ReconstructionModuleAdapter method) (scdlkit.models.autoencoder.AutoEncoder method) (scdlkit.models.classifier.MLPClassifier method) (scdlkit.models.denoising.DenoisingAutoEncoder method) (scdlkit.models.transformer.TransformerAutoEncoder method) (scdlkit.models.vae.VariationalAutoEncoder method) G gene_names (scdlkit.foundation.ScGPTPreparedData attribute) (scdlkit.foundation.ScGPTSplitData attribute) gene_overlap_ratio (scdlkit.foundation.ScGPTAnnotationDataReport attribute) H history_frame (scdlkit.training.trainer.Trainer property) I IA3Config (class in scdlkit.foundation) inspect() (scdlkit.AnnotationRunner method) (scdlkit.foundation.ScGPTAnnotationRunner method) inspect_annotation_data() (in module scdlkit) inspect_scgpt_annotation_data() (in module scdlkit.foundation) L label_categories (scdlkit.foundation.ScGPTAnnotationDataReport attribute) (scdlkit.foundation.ScGPTPreparedData attribute) (scdlkit.foundation.ScGPTSplitData attribute) label_key (scdlkit.foundation.ScGPTAnnotationDataReport attribute) (scdlkit.foundation.ScGPTPreparedData attribute) (scdlkit.foundation.ScGPTSplitData attribute) list_scgpt_checkpoints() (in module scdlkit.foundation) load() (scdlkit.AnnotationRunner class method) (scdlkit.foundation.ScGPTAnnotationRunner class method) load_scgpt_annotation_model() (in module scdlkit.foundation) load_scgpt_model() (in module scdlkit.foundation) LoRAConfig (class in scdlkit.foundation) M min_class_count (scdlkit.foundation.ScGPTAnnotationDataReport attribute) MLPClassifier (class in scdlkit.models.classifier) module scdlkit.models.autoencoder scdlkit.models.classifier scdlkit.models.denoising scdlkit.models.registry scdlkit.models.transformer scdlkit.models.vae N num_cells (scdlkit.foundation.ScGPTAnnotationDataReport attribute) (scdlkit.foundation.ScGPTPreparedData attribute) (scdlkit.foundation.ScGPTSplitData attribute) num_genes_matched (scdlkit.foundation.ScGPTAnnotationDataReport attribute) (scdlkit.foundation.ScGPTPreparedData attribute) (scdlkit.foundation.ScGPTSplitData attribute) num_input_genes (scdlkit.foundation.ScGPTAnnotationDataReport attribute) P PEFTConfig (class in scdlkit.foundation) predict() (scdlkit.AnnotationRunner method) (scdlkit.foundation.ScGPTAnnotationRunner method) (scdlkit.runner.TaskRunner method) predict_batch() (scdlkit.foundation.ScGPTAnnotationModel method) predict_dataset() (scdlkit.training.trainer.Trainer method) PrefixTuningConfig (class in scdlkit.foundation) prepare_data() (in module scdlkit) prepare_scgpt_data() (in module scdlkit.foundation) R reconstruct() (scdlkit.runner.TaskRunner method) ReconstructionModuleAdapter (class in scdlkit.adapters) register_model() (in module scdlkit.models.registry) S save() (scdlkit.AnnotationRunner method) (scdlkit.foundation.ScGPTAnnotationRunner method) save_checkpoint() (scdlkit.training.trainer.Trainer method) save_markdown_report() (in module scdlkit.evaluation) save_metrics_table() (in module scdlkit.evaluation) save_report() (scdlkit.runner.TaskRunner method) scdlkit.models.autoencoder module scdlkit.models.classifier module scdlkit.models.denoising module scdlkit.models.registry module scdlkit.models.transformer module scdlkit.models.vae module ScGPTAnnotationDataReport (class in scdlkit.foundation) ScGPTAnnotationModel (class in scdlkit.foundation) ScGPTAnnotationRunner (class in scdlkit.foundation) ScGPTAnnotationRunSummary (class in scdlkit.foundation) ScGPTEmbeddingModel (class in scdlkit.foundation) ScGPTLoRAConfig (in module scdlkit.foundation) ScGPTPreparedData (class in scdlkit.foundation) ScGPTSplitData (class in scdlkit.foundation) split_scgpt_data() (in module scdlkit.foundation) stratify_possible (scdlkit.foundation.ScGPTAnnotationDataReport attribute) T TaskRunner (class in scdlkit.runner) TorchModuleAdapter (class in scdlkit.adapters) train() (scdlkit.foundation.ScGPTAnnotationModel method) Trainer (class in scdlkit.training.trainer) transform_adata() (in module scdlkit.data.prepare) TransformerAutoEncoder (class in scdlkit.models.transformer) V VariationalAutoEncoder (class in scdlkit.models.vae) W warnings (scdlkit.foundation.ScGPTAnnotationDataReport attribute) wrap_classification_module() (in module scdlkit.adapters) wrap_reconstruction_module() (in module scdlkit.adapters)
