cellarr

• cellarr package
  • Subpackages
    • cellarr.slurm package
      • Submodules
      • 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
      • Module contents
  • Submodules
  • cellarr.CellArrDataset module
    • CellArrCellIterator
      • CellArrCellIterator.__init__()
      • CellArrCellIterator.__iter__()
      • CellArrCellIterator.__next__()
    • CellArrDataset
      • CellArrDataset.__del__()
      • CellArrDataset.__enter__()
      • CellArrDataset.__exit__()
      • CellArrDataset.__getitem__()
      • CellArrDataset.__init__()
      • CellArrDataset.__len__()
      • CellArrDataset.__repr__()
      • CellArrDataset.get_cell_metadata_column()
      • CellArrDataset.get_cell_metadata_columns()
      • CellArrDataset.get_cell_subset()
      • CellArrDataset.get_cells_for_sample()
      • CellArrDataset.get_gene_annotation_column()
      • CellArrDataset.get_gene_annotation_columns()
      • CellArrDataset.get_gene_annotation_index()
      • CellArrDataset.get_gene_subset()
      • CellArrDataset.get_matrix_subset()
      • CellArrDataset.get_number_of_cells()
      • CellArrDataset.get_number_of_features()
      • CellArrDataset.get_number_of_samples()
      • CellArrDataset.get_sample_metadata_column()
      • CellArrDataset.get_sample_metadata_columns()
      • CellArrDataset.get_sample_metadata_index()
      • CellArrDataset.get_sample_subset()
      • CellArrDataset.get_slice()
      • CellArrDataset.itercells()
      • CellArrDataset.itersamples()
      • CellArrDataset.shape
    • CellArrSampleIterator
      • CellArrSampleIterator.__init__()
      • CellArrSampleIterator.__iter__()
      • CellArrSampleIterator.__next__()
  • cellarr.CellArrDatasetSlice module
    • CellArrDatasetSlice
      • CellArrDatasetSlice.__annotations__
      • CellArrDatasetSlice.__dataclass_fields__
      • CellArrDatasetSlice.__dataclass_params__
      • CellArrDatasetSlice.__eq__()
      • CellArrDatasetSlice.__hash__
      • CellArrDatasetSlice.__init__()
      • CellArrDatasetSlice.__len__()
      • CellArrDatasetSlice.__match_args__
      • CellArrDatasetSlice.__repr__()
      • CellArrDatasetSlice.cell_metadata
      • CellArrDatasetSlice.gene_annotation
      • CellArrDatasetSlice.get_assays()
      • CellArrDatasetSlice.matrix
      • CellArrDatasetSlice.shape
      • CellArrDatasetSlice.to_anndata()
      • CellArrDatasetSlice.to_summarizedexperiment()
  • cellarr.autoencoder module
    • AutoEncoder
      • AutoEncoder.__annotations__
      • AutoEncoder.__init__()
      • AutoEncoder.configure_optimizers()
      • AutoEncoder.forward()
      • AutoEncoder.get_loss()
      • AutoEncoder.load_state()
      • AutoEncoder.on_validation_epoch_end()
      • AutoEncoder.on_validation_epoch_start()
      • AutoEncoder.save_all()
      • AutoEncoder.training_step()
      • AutoEncoder.validation_step()
    • Decoder
      • Decoder.__annotations__
      • Decoder.__init__()
      • Decoder.forward()
      • Decoder.load_state()
      • Decoder.save_state()
    • Encoder
      • Encoder.__annotations__
      • Encoder.__init__()
      • Encoder.forward()
      • Encoder.load_state()
      • Encoder.save_state()
  • cellarr.build_cellarrdataset module
    • build_cellarrdataset()
    • generate_metadata_tiledb_csv()
    • generate_metadata_tiledb_frame()
  • cellarr.build_options module
    • CellMetadataOptions
      • CellMetadataOptions.skip
      • CellMetadataOptions.dtype
      • CellMetadataOptions.tiledb_store_name
      • CellMetadataOptions.column_names
      • CellMetadataOptions.column_types
      • CellMetadataOptions.__annotations__
      • CellMetadataOptions.__dataclass_fields__
      • CellMetadataOptions.__dataclass_params__
      • CellMetadataOptions.__eq__()
      • CellMetadataOptions.__hash__
      • CellMetadataOptions.__init__()
      • CellMetadataOptions.__match_args__
      • CellMetadataOptions.__repr__()
      • CellMetadataOptions.column_types
      • CellMetadataOptions.dtype
      • CellMetadataOptions.skip
      • CellMetadataOptions.tiledb_store_name
    • GeneAnnotationOptions
      • GeneAnnotationOptions.feature_column
      • GeneAnnotationOptions.skip
      • GeneAnnotationOptions.dtype
      • GeneAnnotationOptions.tiledb_store_name
      • GeneAnnotationOptions.column_types
      • GeneAnnotationOptions.__annotations__
      • GeneAnnotationOptions.__dataclass_fields__
      • GeneAnnotationOptions.__dataclass_params__
      • GeneAnnotationOptions.__eq__()
      • GeneAnnotationOptions.__hash__
      • GeneAnnotationOptions.__init__()
      • GeneAnnotationOptions.__match_args__
      • GeneAnnotationOptions.__repr__()
      • GeneAnnotationOptions.column_types
      • GeneAnnotationOptions.dtype
      • GeneAnnotationOptions.feature_column
      • GeneAnnotationOptions.skip
      • GeneAnnotationOptions.tiledb_store_name
    • MatrixOptions
      • MatrixOptions.matrix_name
      • MatrixOptions.matrix_attr_name
      • MatrixOptions.consolidate_duplicate_gene_func
      • MatrixOptions.skip
      • MatrixOptions.dtype
      • MatrixOptions.tiledb_store_name
      • MatrixOptions.__annotations__
      • MatrixOptions.__dataclass_fields__
      • MatrixOptions.__dataclass_params__
      • MatrixOptions.__eq__()
      • MatrixOptions.__hash__
      • MatrixOptions.__init__()
      • MatrixOptions.__match_args__
      • MatrixOptions.__repr__()
      • MatrixOptions.consolidate_duplicate_gene_func()
      • MatrixOptions.dtype
      • MatrixOptions.matrix_attr_name
      • MatrixOptions.matrix_name
      • MatrixOptions.skip
      • MatrixOptions.tiledb_store_name
    • SampleMetadataOptions
      • SampleMetadataOptions.skip
      • SampleMetadataOptions.dtype
      • SampleMetadataOptions.tiledb_store_name
      • SampleMetadataOptions.column_types
      • SampleMetadataOptions.__annotations__
      • SampleMetadataOptions.__dataclass_fields__
      • SampleMetadataOptions.__dataclass_params__
      • SampleMetadataOptions.__eq__()
      • SampleMetadataOptions.__hash__
      • SampleMetadataOptions.__init__()
      • SampleMetadataOptions.__match_args__
      • SampleMetadataOptions.__repr__()
      • SampleMetadataOptions.column_types
      • SampleMetadataOptions.dtype
      • SampleMetadataOptions.skip
      • SampleMetadataOptions.tiledb_store_name
  • cellarr.buildutils_tiledb_array module
    • create_group()
    • create_tiledb_array()
    • optimize_tiledb_array()
    • write_csr_matrix_to_tiledb()
  • cellarr.buildutils_tiledb_frame module
    • append_to_tiledb_frame()
    • create_tiledb_frame_from_chunk()
    • create_tiledb_frame_from_column_names()
    • create_tiledb_frame_from_dataframe()
    • infer_column_types()
  • cellarr.dataloader module
    • BaseBatchSampler
      • BaseBatchSampler.__init__()
      • BaseBatchSampler.__iter__()
      • BaseBatchSampler.__len__()
      • BaseBatchSampler.__orig_bases__
      • BaseBatchSampler.__parameters__
    • DataModule
      • DataModule.__annotations__
      • DataModule.__del__()
      • DataModule.__init__()
      • DataModule.__repr__()
      • DataModule.collate()
      • DataModule.filter_db()
      • DataModule.train_dataloader()
      • DataModule.val_dataloader()
    • scDataset
      • scDataset.__annotations__
      • scDataset.__getitem__()
      • scDataset.__init__()
      • scDataset.__len__()
      • scDataset.__parameters__
      • scDataset.__repr__()
  • cellarr.queryutils_tiledb_frame module
    • get_a_column()
    • get_index()
    • get_schema_names_frame()
    • subset_array()
    • subset_frame()
  • cellarr.utils_anndata module
    • consolidate_duplicate_symbols()
    • extract_anndata_info()
    • remap_anndata()
    • scan_for_cellcounts()
    • scan_for_cellmetadata()
    • scan_for_features()
    • scan_for_features_annotations()
  • Module contents