Index _ | A | B | C | D | E | F | G | I | L | M | O | P | R | S | T | V | W _ __annotations__ (cellarr.autoencoder.AutoEncoder attribute) (cellarr.autoencoder.Decoder attribute) (cellarr.autoencoder.Encoder attribute) (cellarr.build_options.CellMetadataOptions attribute) (cellarr.build_options.GeneAnnotationOptions attribute) (cellarr.build_options.MatrixOptions attribute) (cellarr.build_options.SampleMetadataOptions attribute) (cellarr.CellArrDatasetSlice.CellArrDatasetSlice attribute) (cellarr.dataloader.DataModule attribute) (cellarr.dataloader.scDataset attribute) __dataclass_fields__ (cellarr.build_options.CellMetadataOptions attribute) (cellarr.build_options.GeneAnnotationOptions attribute) (cellarr.build_options.MatrixOptions attribute) (cellarr.build_options.SampleMetadataOptions attribute) (cellarr.CellArrDatasetSlice.CellArrDatasetSlice attribute) __dataclass_params__ (cellarr.build_options.CellMetadataOptions attribute) (cellarr.build_options.GeneAnnotationOptions attribute) (cellarr.build_options.MatrixOptions attribute) (cellarr.build_options.SampleMetadataOptions attribute) (cellarr.CellArrDatasetSlice.CellArrDatasetSlice attribute) __del__() (cellarr.CellArrDataset.CellArrDataset method) (cellarr.dataloader.DataModule method) __enter__() (cellarr.CellArrDataset.CellArrDataset method) __eq__() (cellarr.build_options.CellMetadataOptions method) (cellarr.build_options.GeneAnnotationOptions method) (cellarr.build_options.MatrixOptions method) (cellarr.build_options.SampleMetadataOptions method) (cellarr.CellArrDatasetSlice.CellArrDatasetSlice method) __exit__() (cellarr.CellArrDataset.CellArrDataset method) __getitem__() (cellarr.CellArrDataset.CellArrDataset method) (cellarr.dataloader.scDataset method) __hash__ (cellarr.build_options.CellMetadataOptions attribute) (cellarr.build_options.GeneAnnotationOptions attribute) (cellarr.build_options.MatrixOptions attribute) (cellarr.build_options.SampleMetadataOptions attribute) (cellarr.CellArrDatasetSlice.CellArrDatasetSlice attribute) __init__() (cellarr.autoencoder.AutoEncoder method) (cellarr.autoencoder.Decoder method) (cellarr.autoencoder.Encoder method) (cellarr.build_options.CellMetadataOptions method) (cellarr.build_options.GeneAnnotationOptions method) (cellarr.build_options.MatrixOptions method) (cellarr.build_options.SampleMetadataOptions method) (cellarr.CellArrDataset.CellArrCellIterator method) (cellarr.CellArrDataset.CellArrDataset method) (cellarr.CellArrDataset.CellArrSampleIterator method) (cellarr.CellArrDatasetSlice.CellArrDatasetSlice method) (cellarr.dataloader.BaseBatchSampler method) (cellarr.dataloader.DataModule method) (cellarr.dataloader.scDataset method) (cellarr.slurm.build_cellarr_steps.SlurmBuilder method) __iter__() (cellarr.CellArrDataset.CellArrCellIterator method) (cellarr.CellArrDataset.CellArrSampleIterator method) (cellarr.dataloader.BaseBatchSampler method) __len__() (cellarr.CellArrDataset.CellArrDataset method) (cellarr.CellArrDatasetSlice.CellArrDatasetSlice method) (cellarr.dataloader.BaseBatchSampler method) (cellarr.dataloader.scDataset method) __match_args__ (cellarr.build_options.CellMetadataOptions attribute) (cellarr.build_options.GeneAnnotationOptions attribute) (cellarr.build_options.MatrixOptions attribute) (cellarr.build_options.SampleMetadataOptions attribute) (cellarr.CellArrDatasetSlice.CellArrDatasetSlice attribute) __next__() (cellarr.CellArrDataset.CellArrCellIterator method) (cellarr.CellArrDataset.CellArrSampleIterator method) __orig_bases__ (cellarr.dataloader.BaseBatchSampler attribute) __parameters__ (cellarr.dataloader.BaseBatchSampler attribute) (cellarr.dataloader.scDataset attribute) __repr__() (cellarr.build_options.CellMetadataOptions method) (cellarr.build_options.GeneAnnotationOptions method) (cellarr.build_options.MatrixOptions method) (cellarr.build_options.SampleMetadataOptions method) (cellarr.CellArrDataset.CellArrDataset method) (cellarr.CellArrDatasetSlice.CellArrDatasetSlice method) (cellarr.dataloader.DataModule method) (cellarr.dataloader.scDataset method) A append_to_tiledb_frame() (in module cellarr.buildutils_tiledb_frame) AutoEncoder (class in cellarr.autoencoder) B BaseBatchSampler (class in cellarr.dataloader) build_cellarrdataset() (in module cellarr.build_cellarrdataset) C cell_metadata (cellarr.CellArrDatasetSlice.CellArrDatasetSlice attribute) cellarr module cellarr.autoencoder module cellarr.build_cellarrdataset module cellarr.build_options module cellarr.buildutils_tiledb_array module cellarr.buildutils_tiledb_frame module cellarr.CellArrDataset module cellarr.CellArrDatasetSlice module cellarr.dataloader module cellarr.queryutils_tiledb_frame module cellarr.slurm module cellarr.slurm.build_cellarr_steps module cellarr.slurm.final_assembly module cellarr.slurm.finalize_matrix module cellarr.slurm.process_cell_metadata module cellarr.slurm.process_gene_annotation module cellarr.slurm.process_matrix module cellarr.slurm.process_matrix_all module cellarr.slurm.process_sample_metadata module cellarr.utils_anndata module CellArrCellIterator (class in cellarr.CellArrDataset) CellArrDataset (class in cellarr.CellArrDataset) CellArrDatasetSlice (class in cellarr.CellArrDatasetSlice) CellArrSampleIterator (class in cellarr.CellArrDataset) CellMetadataOptions (class in cellarr.build_options) collate() (cellarr.dataloader.DataModule method) column_names (cellarr.build_options.CellMetadataOptions attribute) column_types (cellarr.build_options.CellMetadataOptions attribute), [1] (cellarr.build_options.GeneAnnotationOptions attribute), [1] (cellarr.build_options.SampleMetadataOptions attribute), [1] configure_optimizers() (cellarr.autoencoder.AutoEncoder method) consolidate_duplicate_gene_func (cellarr.build_options.MatrixOptions attribute) consolidate_duplicate_gene_func() (cellarr.build_options.MatrixOptions method) consolidate_duplicate_symbols() (in module cellarr.utils_anndata) create_array_script() (cellarr.slurm.build_cellarr_steps.SlurmBuilder method) create_group() (in module cellarr.buildutils_tiledb_array) create_slurm_script() (cellarr.slurm.build_cellarr_steps.SlurmBuilder method) create_tiledb_array() (in module cellarr.buildutils_tiledb_array) create_tiledb_frame_from_chunk() (in module cellarr.buildutils_tiledb_frame) create_tiledb_frame_from_column_names() (in module cellarr.buildutils_tiledb_frame) create_tiledb_frame_from_dataframe() (in module cellarr.buildutils_tiledb_frame) D DataModule (class in cellarr.dataloader) Decoder (class in cellarr.autoencoder) dtype (cellarr.build_options.CellMetadataOptions attribute), [1] (cellarr.build_options.GeneAnnotationOptions attribute), [1] (cellarr.build_options.MatrixOptions attribute), [1] (cellarr.build_options.SampleMetadataOptions attribute), [1] E Encoder (class in cellarr.autoencoder) extract_anndata_info() (in module cellarr.utils_anndata) F feature_column (cellarr.build_options.GeneAnnotationOptions attribute), [1] filter_db() (cellarr.dataloader.DataModule method) final_assembly() (in module cellarr.slurm.final_assembly) finalize_matrix() (in module cellarr.slurm.finalize_matrix) forward() (cellarr.autoencoder.AutoEncoder method) (cellarr.autoencoder.Decoder method) (cellarr.autoencoder.Encoder method) G gene_annotation (cellarr.CellArrDatasetSlice.CellArrDatasetSlice attribute) GeneAnnotationOptions (class in cellarr.build_options) generate_metadata_tiledb_csv() (in module cellarr.build_cellarrdataset) generate_metadata_tiledb_frame() (in module cellarr.build_cellarrdataset) get_a_column() (in module cellarr.queryutils_tiledb_frame) get_assays() (cellarr.CellArrDatasetSlice.CellArrDatasetSlice method) get_cell_metadata_column() (cellarr.CellArrDataset.CellArrDataset method) get_cell_metadata_columns() (cellarr.CellArrDataset.CellArrDataset method) get_cell_subset() (cellarr.CellArrDataset.CellArrDataset method) get_cells_for_sample() (cellarr.CellArrDataset.CellArrDataset method) get_gene_annotation_column() (cellarr.CellArrDataset.CellArrDataset method) get_gene_annotation_columns() (cellarr.CellArrDataset.CellArrDataset method) get_gene_annotation_index() (cellarr.CellArrDataset.CellArrDataset method) get_gene_subset() (cellarr.CellArrDataset.CellArrDataset method) get_index() (in module cellarr.queryutils_tiledb_frame) get_loss() (cellarr.autoencoder.AutoEncoder method) get_matrix_subset() (cellarr.CellArrDataset.CellArrDataset method) get_number_of_cells() (cellarr.CellArrDataset.CellArrDataset method) get_number_of_features() (cellarr.CellArrDataset.CellArrDataset method) get_number_of_samples() (cellarr.CellArrDataset.CellArrDataset method) get_sample_metadata_column() (cellarr.CellArrDataset.CellArrDataset method) get_sample_metadata_columns() (cellarr.CellArrDataset.CellArrDataset method) get_sample_metadata_index() (cellarr.CellArrDataset.CellArrDataset method) get_sample_subset() (cellarr.CellArrDataset.CellArrDataset method) get_schema_names_frame() (in module cellarr.queryutils_tiledb_frame) get_slice() (cellarr.CellArrDataset.CellArrDataset method) I infer_column_types() (in module cellarr.buildutils_tiledb_frame) itercells() (cellarr.CellArrDataset.CellArrDataset method) itersamples() (cellarr.CellArrDataset.CellArrDataset method) L load_state() (cellarr.autoencoder.AutoEncoder method) (cellarr.autoencoder.Decoder method) (cellarr.autoencoder.Encoder method) M main() (in module cellarr.slurm.build_cellarr_steps) matrix (cellarr.CellArrDatasetSlice.CellArrDatasetSlice attribute) matrix_attr_name (cellarr.build_options.MatrixOptions attribute), [1] matrix_name (cellarr.build_options.MatrixOptions attribute), [1] MatrixOptions (class in cellarr.build_options) module cellarr cellarr.autoencoder cellarr.build_cellarrdataset cellarr.build_options cellarr.buildutils_tiledb_array cellarr.buildutils_tiledb_frame cellarr.CellArrDataset cellarr.CellArrDatasetSlice cellarr.dataloader cellarr.queryutils_tiledb_frame cellarr.slurm cellarr.slurm.build_cellarr_steps cellarr.slurm.final_assembly cellarr.slurm.finalize_matrix cellarr.slurm.process_cell_metadata cellarr.slurm.process_gene_annotation cellarr.slurm.process_matrix cellarr.slurm.process_matrix_all cellarr.slurm.process_sample_metadata cellarr.utils_anndata O on_validation_epoch_end() (cellarr.autoencoder.AutoEncoder method) on_validation_epoch_start() (cellarr.autoencoder.AutoEncoder method) optimize_tiledb_array() (in module cellarr.buildutils_tiledb_array) P process_cell_metadata() (in module cellarr.slurm.process_cell_metadata) process_gene_annotation() (in module cellarr.slurm.process_gene_annotation) process_matrix() (in module cellarr.slurm.process_matrix_all) process_matrix_file() (in module cellarr.slurm.process_matrix) process_sample_metadata() (in module cellarr.slurm.process_sample_metadata) R remap_anndata() (in module cellarr.utils_anndata) S SampleMetadataOptions (class in cellarr.build_options) save_all() (cellarr.autoencoder.AutoEncoder method) save_state() (cellarr.autoencoder.Decoder method) (cellarr.autoencoder.Encoder method) scan_for_cellcounts() (in module cellarr.utils_anndata) scan_for_cellmetadata() (in module cellarr.utils_anndata) scan_for_features() (in module cellarr.utils_anndata) scan_for_features_annotations() (in module cellarr.utils_anndata) scDataset (class in cellarr.dataloader) shape (cellarr.CellArrDataset.CellArrDataset property) (cellarr.CellArrDatasetSlice.CellArrDatasetSlice property) skip (cellarr.build_options.CellMetadataOptions attribute), [1] (cellarr.build_options.GeneAnnotationOptions attribute), [1] (cellarr.build_options.MatrixOptions attribute), [1] (cellarr.build_options.SampleMetadataOptions attribute), [1] SlurmBuilder (class in cellarr.slurm.build_cellarr_steps) submit_cell_metadata_job() (cellarr.slurm.build_cellarr_steps.SlurmBuilder method) submit_final_assembly() (cellarr.slurm.build_cellarr_steps.SlurmBuilder method) submit_gene_annotation_job() (cellarr.slurm.build_cellarr_steps.SlurmBuilder method) submit_job() (cellarr.slurm.build_cellarr_steps.SlurmBuilder method) submit_matrix_processing() (cellarr.slurm.build_cellarr_steps.SlurmBuilder method) submit_sample_metadata_job() (cellarr.slurm.build_cellarr_steps.SlurmBuilder method) subset_array() (in module cellarr.queryutils_tiledb_frame) subset_frame() (in module cellarr.queryutils_tiledb_frame) T tiledb_store_name (cellarr.build_options.CellMetadataOptions attribute), [1] (cellarr.build_options.GeneAnnotationOptions attribute), [1] (cellarr.build_options.MatrixOptions attribute), [1] (cellarr.build_options.SampleMetadataOptions attribute), [1] to_anndata() (cellarr.CellArrDatasetSlice.CellArrDatasetSlice method) to_summarizedexperiment() (cellarr.CellArrDatasetSlice.CellArrDatasetSlice method) train_dataloader() (cellarr.dataloader.DataModule method) training_step() (cellarr.autoencoder.AutoEncoder method) V val_dataloader() (cellarr.dataloader.DataModule method) validation_step() (cellarr.autoencoder.AutoEncoder method) W write_csr_matrix_to_tiledb() (in module cellarr.buildutils_tiledb_array)