Index

_

_get_datapath_from_config() (in module scalr.utils.file_utils) _is_shap_early_stop() (scalr.feature.scoring.shap_scorer.ShapScorer method) _make_design_matrix() (scalr.analysis.dge_pseudobulk.DgePseudoBulk method)

_perform_downstream_analysis() (scalr.eval_and_analysis_pipeline.EvalAndAnalysisPipeline method) _split_data_with_stratification() (scalr.data.split.group_splitter.GroupSplitter method) (scalr.data.split.stratified_group_splitter.StratifiedGroupSplitter method) (scalr.data.split.stratified_splitter.StratifiedSplitter method)

A

AbsMean (class in scalr.feature.selector.abs_mean)

AnalysisBase (class in scalr.analysis._analyser)

B

build_analyser() (in module scalr.analysis._analyser) build_dataloader() (in module scalr.nn.dataloader._dataloader) build_dataloaders() (scalr.eval_and_analysis_pipeline.EvalAndAnalysisPipeline method) build_loss_fn() (in module scalr.nn.loss._loss) build_model() (in module scalr.nn.model._model) build_model_training_artifacts() (scalr.model_training_pipeline.ModelTrainingPipeline method)

build_object() (in module scalr.utils.misc_utils) build_optimizer() (scalr.model_training_pipeline.ModelTrainingPipeline method) build_preprocessor() (in module scalr.data.preprocess._preprocess) build_scorer() (in module scalr.feature.scoring._scoring) build_selector() (in module scalr.feature.selector._selector) build_splitter() (in module scalr.data.split._split)

C

calculate_mean() (scalr.data.preprocess.standard_scale.StandardScaler method) calculate_std() (scalr.data.preprocess.standard_scale.StandardScaler method) CallbackBase (class in scalr.nn.callbacks._callbacks) CallbackExecutor (class in scalr.nn.callbacks._callbacks) check_splits() (scalr.data.split._split.SplitterBase method) ClasswiseAbs (class in scalr.feature.selector.classwise_abs)

ClasswisePromoters (class in scalr.feature.selector.classwise_promoters) collate_fn() (scalr.nn.dataloader._dataloader.DataLoaderBase method) (scalr.nn.dataloader.simple_dataloader.SimpleDataLoader method) (scalr.nn.dataloader.simple_metadataloader.SimpleMetaDataLoader method) CustomLossBase (class in scalr.nn.loss._loss) CustomShapModel (class in scalr.nn.model.shap_model)

D

DataIngestionPipeline (class in scalr.data_ingestion_pipeline) DataLoaderBase (class in scalr.nn.dataloader._dataloader) DgeLMEM (class in scalr.analysis.dge_lmem) DgePseudoBulk (class in scalr.analysis.dge_pseudobulk)

dump_anndata() (in module scalr.utils.file_utils) dump_csv() (in module scalr.utils.file_utils) dump_json() (in module scalr.utils.file_utils) dump_yaml() (in module scalr.utils.file_utils)

E

EarlyStopping (class in scalr.nn.callbacks.early_stopping) epoch (scalr.nn.callbacks.model_checkpoint.ModelCheckpoint attribute) (scalr.nn.callbacks.tensorboard_logger.TensorboardLogger attribute)

EvalAndAnalysisPipeline (class in scalr.eval_and_analysis_pipeline) evaluation_and_classification_report() (scalr.eval_and_analysis_pipeline.EvalAndAnalysisPipeline method) EventLogger (class in scalr.utils.logger) execute() (scalr.nn.callbacks._callbacks.CallbackExecutor method)

F

feature_scoring() (scalr.feature_extraction_pipeline.FeatureExtractionPipeline method) feature_subsetted_model_training() (scalr.feature_extraction_pipeline.FeatureExtractionPipeline method) FeatureExtractionPipeline (class in scalr.feature_extraction_pipeline) FeatureSubsetting (class in scalr.feature.feature_subsetting) filepath (scalr.utils.logger.EventLogger attribute) fit() (scalr.data.preprocess._preprocess.PreprocessorBase method) (scalr.data.preprocess.standard_scale.StandardScaler method)

FlowLogger (class in scalr.utils.logger) forward() (scalr.nn.loss._loss.CustomLossBase method) (scalr.nn.model._model.ModelBase method) (scalr.nn.model.sequential_model.SequentialModel method) (scalr.nn.model.shap_model.CustomShapModel method) full_samples_downstream_anlaysis() (scalr.eval_and_analysis_pipeline.EvalAndAnalysisPipeline method)

G

gene_analysis() (scalr.eval_and_analysis_pipeline.EvalAndAnalysisPipeline method) generate_analysis() (scalr.analysis._analyser.AnalysisBase method) (scalr.analysis.dge_lmem.DgeLMEM method) (scalr.analysis.dge_pseudobulk.DgePseudoBulk method) (scalr.analysis.gene_recall_curve.GeneRecallCurve method) (scalr.analysis.heatmap.Heatmap method) (scalr.analysis.roc_auc.RocAucCurve method) generate_and_save_classification_report() (in module scalr.analysis.evaluation) generate_dummy_anndata() (in module scalr.utils.data_utils) generate_dummy_dge_anndata() (in module scalr.utils.data_utils) generate_mappings() (scalr.data_ingestion_pipeline.DataIngestionPipeline method) generate_scores() (scalr.feature.scoring._scoring.ScoringBase method) (scalr.feature.scoring.linear_scorer.LinearScorer method) (scalr.feature.scoring.shap_scorer.ShapScorer method) generate_train_val_test_split() (scalr.data_ingestion_pipeline.DataIngestionPipeline method) generate_train_val_test_split_indices() (scalr.data.split._split.SplitterBase method) (scalr.data.split.stratified_group_splitter.StratifiedGroupSplitter method) (scalr.data.split.stratified_splitter.StratifiedSplitter method) GeneRecallCurve (class in scalr.analysis.gene_recall_curve) get_accuracy() (in module scalr.analysis.evaluation) get_default_params() (scalr.analysis._analyser.AnalysisBase class method) (scalr.analysis.dge_lmem.DgeLMEM class method) (scalr.analysis.dge_pseudobulk.DgePseudoBulk class method) (scalr.analysis.gene_recall_curve.GeneRecallCurve class method) (scalr.data.preprocess.sample_norm.SampleNorm class method) (scalr.data.preprocess.standard_scale.StandardScaler class method) (scalr.data.split._split.SplitterBase class method) (scalr.data.split.group_splitter.GroupSplitter class method) (scalr.data.split.stratified_group_splitter.StratifiedGroupSplitter class method) (scalr.data.split.stratified_splitter.StratifiedSplitter class method) (scalr.feature.scoring._scoring.ScoringBase class method) (scalr.feature.scoring.shap_scorer.ShapScorer class method) (scalr.feature.selector._selector.SelectorBase class method) (scalr.feature.selector.abs_mean.AbsMean class method) (scalr.feature.selector.classwise_abs.ClasswiseAbs class method) (scalr.feature.selector.classwise_promoters.ClasswisePromoters class method) (scalr.nn.callbacks._callbacks.CallbackBase class method) (scalr.nn.callbacks.early_stopping.EarlyStopping class method) (scalr.nn.callbacks.model_checkpoint.ModelCheckpoint class method) (scalr.nn.callbacks.tensorboard_logger.TensorboardLogger class method) (scalr.nn.dataloader._dataloader.DataLoaderBase class method) (scalr.nn.dataloader.simple_dataloader.SimpleDataLoader class method) (scalr.nn.dataloader.simple_metadataloader.SimpleMetaDataLoader class method) (scalr.nn.model._model.ModelBase class method) (scalr.nn.model.sequential_model.SequentialModel class method)

get_differential_expression_results() (scalr.analysis.dge_pseudobulk.DgePseudoBulk method) get_feature_list() (scalr.feature.selector._selector.SelectorBase method) (scalr.feature.selector.abs_mean.AbsMean method) (scalr.feature.selector.classwise_abs.ClasswiseAbs method) (scalr.feature.selector.classwise_promoters.ClasswisePromoters method) get_genes_n_fixed_val_subset_df() (scalr.analysis.dge_lmem.DgeLMEM method) get_multiproc_mxeffect_model_batch_res() (scalr.analysis.dge_lmem.DgeLMEM method) get_one_hot_matrix() (in module scalr.utils.data_utils) get_predictions() (scalr.nn.model._model.ModelBase method) (scalr.nn.model.sequential_model.SequentialModel method) get_random_samples() (in module scalr.utils.data_utils) get_result_mxmodel_per_gene() (scalr.analysis.dge_lmem.DgeLMEM method) get_targets_ids_from_mappings() (scalr.nn.dataloader._dataloader.DataLoaderBase method) get_top_n_genes_weights() (scalr.feature.scoring.shap_scorer.ShapScorer method) get_updated_config() (scalr.data_ingestion_pipeline.DataIngestionPipeline method) (scalr.eval_and_analysis_pipeline.EvalAndAnalysisPipeline method) (scalr.feature_extraction_pipeline.FeatureExtractionPipeline method) (scalr.model_training_pipeline.ModelTrainingPipeline method) get_updated_configs() (scalr.feature.feature_subsetting.FeatureSubsetting method) GroupSplitter (class in scalr.data.split.group_splitter)

H

heading() (scalr.utils.logger.EventLogger method) heading1() (scalr.utils.logger.EventLogger method)

heading2() (scalr.utils.logger.EventLogger method) Heatmap (class in scalr.analysis.heatmap)

I

interval (scalr.nn.callbacks.model_checkpoint.ModelCheckpoint attribute)

L

level (scalr.utils.logger.EventLogger attribute) (scalr.utils.logger.FlowLogger attribute) LinearScorer (class in scalr.feature.scoring.linear_scorer) load_data_and_targets_from_config() (scalr.eval_and_analysis_pipeline.EvalAndAnalysisPipeline method) (scalr.feature_extraction_pipeline.FeatureExtractionPipeline method) (scalr.model_training_pipeline.ModelTrainingPipeline method)

load_full_data_from_config() (in module scalr.utils.file_utils) load_test_data_from_config() (in module scalr.utils.file_utils) load_train_val_data_from_config() (in module scalr.utils.file_utils) load_weights() (scalr.nn.model._model.ModelBase method)

M

make_weights_zero() (scalr.nn.model.sequential_model.SequentialModel method) max_validation_acc (scalr.nn.callbacks.model_checkpoint.ModelCheckpoint attribute) min_delta (scalr.nn.callbacks.early_stopping.EarlyStopping attribute) ModelBase (class in scalr.nn.model._model) ModelCheckpoint (class in scalr.nn.callbacks.model_checkpoint) ModelTrainingPipeline (class in scalr.model_training_pipeline) module scalr.analysis._analyser scalr.analysis.dge_lmem scalr.analysis.dge_pseudobulk scalr.analysis.evaluation scalr.analysis.gene_recall_curve scalr.analysis.heatmap scalr.analysis.roc_auc scalr.data.preprocess._preprocess scalr.data.preprocess.sample_norm scalr.data.preprocess.standard_scale scalr.data.preprocess.test_sample_norm scalr.data.preprocess.test_standard_scale scalr.data.split._split scalr.data.split.group_splitter scalr.data.split.stratified_group_splitter scalr.data.split.stratified_splitter scalr.data_ingestion_pipeline scalr.eval_and_analysis_pipeline scalr.feature.feature_subsetting scalr.feature.scoring._scoring scalr.feature.scoring.linear_scorer scalr.feature.scoring.shap_scorer scalr.feature.selector._selector scalr.feature.selector.abs_mean scalr.feature.selector.classwise_abs scalr.feature.selector.classwise_promoters scalr.feature_extraction_pipeline scalr.model_training_pipeline scalr.nn.callbacks._callbacks scalr.nn.callbacks.early_stopping scalr.nn.callbacks.model_checkpoint scalr.nn.callbacks.tensorboard_logger scalr.nn.callbacks.test_early_stopping scalr.nn.dataloader._dataloader scalr.nn.dataloader.simple_dataloader scalr.nn.dataloader.simple_metadataloader scalr.nn.dataloader.test_simple_dataloader scalr.nn.dataloader.test_simple_metadataloader scalr.nn.loss._loss scalr.nn.model._model scalr.nn.model.sequential_model scalr.nn.model.shap_model scalr.nn.trainer._trainer scalr.nn.trainer.simple_model_trainer scalr.utils.data_utils scalr.utils.file_utils scalr.utils.logger scalr.utils.misc_utils scalr.utils.test_file_utils scalr.utils.test_misc_utils

O

overwrite_default() (in module scalr.utils.misc_utils)

P

patience (scalr.nn.callbacks.early_stopping.EarlyStopping attribute) plot_gene_recall() (scalr.analysis.gene_recall_curve.GeneRecallCurve method) plot_heatmap() (scalr.analysis.heatmap.Heatmap method) plot_lmem_dge_result() (scalr.analysis.dge_lmem.DgeLMEM method)

plot_volcano() (scalr.analysis.dge_pseudobulk.DgePseudoBulk method) preprocess_data() (scalr.data_ingestion_pipeline.DataIngestionPipeline method) PreprocessorBase (class in scalr.data.preprocess._preprocess) process_data() (scalr.data.preprocess._preprocess.PreprocessorBase method)

R

read_anndata() (in module scalr.utils.file_utils) read_chunked_anndatas() (in module scalr.utils.file_utils) read_csv() (in module scalr.utils.file_utils) read_data() (in module scalr.utils.file_utils)

read_json() (in module scalr.utils.file_utils) read_yaml() (in module scalr.utils.file_utils) replace_spec_char_get_dict() (scalr.analysis.dge_lmem.DgeLMEM method) RocAucCurve (class in scalr.analysis.roc_auc)

S

SampleNorm (class in scalr.data.preprocess.sample_norm) save_checkpoint() (scalr.nn.callbacks.model_checkpoint.ModelCheckpoint method) save_weights() (scalr.nn.model._model.ModelBase method) scalr.analysis._analyser module scalr.analysis.dge_lmem module scalr.analysis.dge_pseudobulk module scalr.analysis.evaluation module scalr.analysis.gene_recall_curve module scalr.analysis.heatmap module scalr.analysis.roc_auc module scalr.data.preprocess._preprocess module scalr.data.preprocess.sample_norm module scalr.data.preprocess.standard_scale module scalr.data.preprocess.test_sample_norm module scalr.data.preprocess.test_standard_scale module scalr.data.split._split module scalr.data.split.group_splitter module scalr.data.split.stratified_group_splitter module scalr.data.split.stratified_splitter module scalr.data_ingestion_pipeline module scalr.eval_and_analysis_pipeline module scalr.feature.feature_subsetting module scalr.feature.scoring._scoring module scalr.feature.scoring.linear_scorer module scalr.feature.scoring.shap_scorer module scalr.feature.selector._selector module scalr.feature.selector.abs_mean module scalr.feature.selector.classwise_abs module scalr.feature.selector.classwise_promoters module scalr.feature_extraction_pipeline module scalr.model_training_pipeline module scalr.nn.callbacks._callbacks module

scalr.nn.callbacks.early_stopping module scalr.nn.callbacks.model_checkpoint module scalr.nn.callbacks.tensorboard_logger module scalr.nn.callbacks.test_early_stopping module scalr.nn.dataloader._dataloader module scalr.nn.dataloader.simple_dataloader module scalr.nn.dataloader.simple_metadataloader module scalr.nn.dataloader.test_simple_dataloader module scalr.nn.dataloader.test_simple_metadataloader module scalr.nn.loss._loss module scalr.nn.model._model module scalr.nn.model.sequential_model module scalr.nn.model.shap_model module scalr.nn.trainer._trainer module scalr.nn.trainer.simple_model_trainer module scalr.utils.data_utils module scalr.utils.file_utils module scalr.utils.logger module scalr.utils.misc_utils module scalr.utils.test_file_utils module scalr.utils.test_misc_utils module ScoringBase (class in scalr.feature.scoring._scoring) SelectorBase (class in scalr.feature.selector._selector) SequentialModel (class in scalr.nn.model.sequential_model) set_data_and_targets() (scalr.eval_and_analysis_pipeline.EvalAndAnalysisPipeline method) (scalr.feature_extraction_pipeline.FeatureExtractionPipeline method) (scalr.model_training_pipeline.ModelTrainingPipeline method) set_model() (scalr.feature_extraction_pipeline.FeatureExtractionPipeline method) set_score_matrix() (scalr.feature_extraction_pipeline.FeatureExtractionPipeline method) set_seed() (in module scalr.utils.misc_utils) ShapScorer (class in scalr.feature.scoring.shap_scorer) SimpleDataLoader (class in scalr.nn.dataloader.simple_dataloader) SimpleMetaDataLoader (class in scalr.nn.dataloader.simple_metadataloader) SimpleModelTrainer (class in scalr.nn.trainer.simple_model_trainer) SplitterBase (class in scalr.data.split._split) StandardScaler (class in scalr.data.preprocess.standard_scale) StratifiedGroupSplitter (class in scalr.data.split.stratified_group_splitter) StratifiedSplitter (class in scalr.data.split.stratified_splitter)

T

TensorboardLogger (class in scalr.nn.callbacks.tensorboard_logger) test_early_stopping() (in module scalr.nn.callbacks.test_early_stopping) test_fit() (in module scalr.data.preprocess.test_standard_scale) test_metadataloader() (in module scalr.nn.dataloader.test_simple_dataloader) (in module scalr.nn.dataloader.test_simple_metadataloader) test_overwrite_default() (in module scalr.utils.test_misc_utils) test_samples_downstream_anlaysis() (scalr.eval_and_analysis_pipeline.EvalAndAnalysisPipeline method) test_transform() (in module scalr.data.preprocess.test_sample_norm) test_write_chunkwise_data() (in module scalr.utils.test_file_utils)

top_feature_extraction() (scalr.feature_extraction_pipeline.FeatureExtractionPipeline method) train() (scalr.model_training_pipeline.ModelTrainingPipeline method) (scalr.nn.trainer._trainer.TrainerBase method) train_chunked_models() (scalr.feature.feature_subsetting.FeatureSubsetting method) train_one_epoch() (scalr.nn.trainer._trainer.TrainerBase method) TrainerBase (class in scalr.nn.trainer._trainer) transform() (scalr.data.preprocess._preprocess.PreprocessorBase method) (scalr.data.preprocess.sample_norm.SampleNorm method) (scalr.data.preprocess.standard_scale.StandardScaler method)

V

validation() (scalr.nn.trainer._trainer.TrainerBase method)

W

write_chunkwise_data() (in module scalr.utils.file_utils) write_data() (in module scalr.utils.file_utils) write_feature_subsetted_data() (scalr.feature.feature_subsetting.FeatureSubsetting method)

write_splits() (scalr.data.split._split.SplitterBase method) write_top_features_subset_data() (scalr.feature_extraction_pipeline.FeatureExtractionPipeline method) writer (scalr.nn.callbacks.tensorboard_logger.TensorboardLogger attribute)