Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | X | Y _ __init__() (malva.compressed_index.CompressedArrayStorage method) (malva.compressed_index.LazyChunkTable method) (malva.dbutils.EnsemblLocalDB method) (malva.serve.reportgen.HTMLReportGenerator method) (malva.serve.serve.GlobalState method) (malva.serve.serve.MalvaProxyFix method) (malva.serve.serve.SequenceValidationError method) (malva.serve.serve.SpatialData method) (malva.serve.serve.UserSession method) (malva.show.MalvaPlot method) (malva.utils.FormatError method) A add() (malva.fast_map.FastMapOfMap method) add_background_data() (malva.serve.serve.UserSession method) add_query_result() (malva.serve.serve.UserSession method) add_reads() (malva.indexes.MalvaIndex method) aggregate_adata_by_indices() (in module malva.spacemake) analyze_technical_genes() (in module malva.autoannotate) annotate_clusters() (in module malva.autoannotate) attrs (malva.datastore.ChunkedStore attribute) B BackgroundModel (class in malva.indexes) binary_search() (in module malva.utils) binning_hexagon() (in module malva.spacemake) bounds (malva.serve.serve.SpatialData attribute) C check_adata_structure() (in module malva.utils) check_cell_string() (in module malva.utils) check_directory_exists() (in module malva.utils) check_file_exists() (in module malva.utils) check_obs_unique() (in module malva.utils) check_server_connection() (in module malva.search) ChunkedStore (class in malva.datastore) cleanup() (malva.serve.serve.UserSession method) clear() (malva.fast_map.FastMapOfMap method) close() (malva.datastore.ChunkedStore method) (malva.indexes.MalvaIndex method) cmd_run_autoannotate() (in module malva.cli) cmd_run_cellxmer() (in module malva.cli) cmd_run_combine() (in module malva.cli) cmd_run_index() (in module malva.cli) cmd_run_quant() (in module malva.cli) cmd_run_search() (in module malva.cli) cmd_run_serve() (in module malva.cli) cmd_run_show() (in module malva.cli) cmdline_args() (in module malva.cli) cmdline_main() (in module malva.cli) cmdline_parser() (in module malva.cli) combine_indices() (in module malva.combine) complexity() (in module malva.complexity) CompressedArrayStorage (class in malva.compressed_index) compute_rep_vector() (in module malva.complexity) conditional_track() (in module malva.utils) contains() (malva.datastore.ChunkedStore method) convert_h5_to_chunked() (in module malva.datastore) convert_to_bytes() (in module malva.utils) coord_lims (malva.indexes.MalvaIndex attribute) coordinates (malva.serve.serve.SpatialData attribute) copy_dataset() (malva.datastore.ChunkedStore method) copytree2() (in module malva.utils) create_app() (in module malva.serve.serve) create_dataset() (malva.datastore.ChunkedStore method) create_from_reference() (malva.indexes.BackgroundModel method) create_mesh() (in module malva.spacemake) create_meshed_adata() (in module malva.spacemake) create_report_zip() (malva.serve.reportgen.HTMLReportGenerator method) create_singlecell_index() (in module malva.indexes) create_spatial_index() (in module malva.indexes) D data_dir (malva.dbutils.EnsemblLocalDB attribute) data_lengths (malva.indexes.MalvaIndex attribute) database_exists() (malva.dbutils.EnsemblLocalDB method) decode_kmer() (in module malva.kmer_processing) defragment_hdf5_file() (in module malva.utils) download_cdna_fasta() (malva.dbutils.EnsemblLocalDB method) download_url_to_file() (in module malva.utils) E EliasPageCache (class in malva.datastore) emptydrops_refinement() (in module malva.autoannotate) encode_kmer() (in module malva.kmer_processing) EnsemblLocalDB (class in malva.dbutils) export_fasta() (malva.indexes.BackgroundModel method) extend() (malva.fast_map.FastMapOfMap method) F FastKmerExtractor (class in malva.kmer_processing) FastKmerProcessor (class in malva.fastq_processing) FastMapOfMap (class in malva.fast_map) filter_kmers() (in module malva.filter_minimizers) filter_stream() (malva.filter_minimizers.KmerFilter method) flush() (malva.datastore.ChunkedStore method) (malva.datastore.PageAlignedArray method) format_results() (in module malva.search) FormatError from_array() (malva.compressed_index.CompressedArrayStorage method) from_generator() (malva.compressed_index.CompressedArrayStorage method) G gene_to_ensembl (malva.dbutils.EnsemblLocalDB attribute) get() (malva.compressed_index.CompressedArrayStorage method) get_absolute_package_path() (in module malva.utils) get_autoannotate_parser() (in module malva.cli) get_batch() (malva.compressed_index.CompressedArrayStorage method) get_bounds() (malva.serve.serve.GlobalState method) get_cache_stats() (malva.compressed_index.CompressedArrayStorage method) get_cell_id() (malva.indexes.MalvaIndex method) get_cellxmer_parser() (in module malva.cli) get_chunk() (malva.compressed_index.CompressedArrayStorage method) get_chunk_for_cython() (malva.compressed_index.CompressedArrayStorage method) get_chunk_indices() (malva.datastore.ChunkedStore method) get_chunk_raw() (malva.compressed_index.CompressedArrayStorage method) get_combine_parser() (in module malva.cli) get_coordinates() (malva.serve.serve.GlobalState method) get_coords() (malva.indexes.SpatialIndex method) get_coords_stomics() (malva.indexes.SpatialIndex method) get_datasets() (in module malva.search) get_detailed_cluster_annotations() (in module malva.autoannotate) get_from_ensembl() (in module malva.dbutils) get_from_gene() (in module malva.dbutils) (malva.dbutils.EnsemblLocalDB method) get_index_parser() (in module malva.cli) get_job_status() (in module malva.search) get_kmers_numeric() (in module malva.kmer_processing) get_module_path() (in module malva.utils) get_multiple_slices() (malva.compressed_index.CompressedArrayStorage method) get_package_path() (in module malva.utils) get_project_id() (malva.indexes.MalvaIndex method) get_quant_parser() (in module malva.cli) get_reference_cache() (in module malva.utils) get_search_parser() (in module malva.cli) get_serve_parser() (in module malva.cli) get_shape() (malva.datastore.PageAlignedArray method) get_show_parser() (in module malva.cli) get_slice() (malva.compressed_index.CompressedArrayStorage method) get_sliding_kmers_numeric() (in module malva.kmer_processing) get_tile_data() (malva.serve.serve.UserSession method) get_top_cell_types() (in module malva.autoannotate) get_whole_sliding_sequence() (malva.indexes.MalvaIndex method) get_whole_sliding_sequence_chunk() (malva.indexes.MalvaIndex method) GlobalState (class in malva.serve.serve) group_intervals() (in module malva.utils) H h5_to_dict() (in module malva.utils) handle_natural_query() (in module malva.serve.modeling) handle_sequence() (in module malva.dbutils) hierarchical_combine() (in module malva.combine) HTMLReportGenerator (class in malva.serve.reportgen) I image() (malva.show.MalvaPlot method) import_jellyfish_fasta() (malva.indexes.BackgroundModel method) index (malva.dbutils.EnsemblLocalDB attribute) (malva.indexes.MalvaIndex attribute) index_dir (malva.indexes.MalvaIndex attribute), [1] index_exists() (malva.indexes.MalvaIndex static method) index_fasta() (malva.dbutils.EnsemblLocalDB method) index_file (malva.indexes.MalvaIndex attribute) initialize() (malva.indexes.MalvaIndex method) (malva.serve.serve.GlobalState method) initialize_background() (malva.serve.serve.UserSession method) initialize_from_index() (malva.serve.serve.GlobalState method) initialize_kmer_index() (malva.indexes.MalvaIndex method) interactive_query_standard() (in module malva.serve.serve) is_mer_above_cutoff() (malva.indexes.BackgroundModel method) items() (malva.datastore.ChunkedStore method) (malva.fast_map.FastMapOfMap method) iterate_fasta() (in module malva.reader) iterate_flavor() (in module malva.reader) J jump_amount (malva.indexes.MalvaIndex attribute) K k (malva.filter_minimizers.KmerFilter attribute), [1] keys() (malva.datastore.ChunkedStore method) kmer_size (malva.fastq_processing.FastKmerProcessor attribute) (malva.indexes.BackgroundModel attribute) (malva.indexes.MalvaIndex attribute), [1] KmerFastqParser (class in malva.fastq_processing) KmerFilter (class in malva.filter_minimizers) L LazyChunkTable (class in malva.compressed_index) load() (malva.compressed_index.CompressedArrayStorage method) (malva.indexes.BackgroundModel method) load_all_chunks_to_memory() (malva.compressed_index.CompressedArrayStorage method) load_binary() (malva.indexes.SpatialIndex method) load_binary_stomics() (malva.indexes.SpatialIndex method) load_flavor() (in module malva.index) load_index() (malva.dbutils.EnsemblLocalDB method) load_index_to_memory() (malva.indexes.MalvaIndex method) load_marker_genes() (in module malva.autoannotate) load_markers() (in module malva.autoannotate) load_pickle() (in module malva.utils) load_properties_from_adata() (in module malva.utils) M malva module malva.autoannotate module malva.cellxmer module malva.cli module malva.combine module malva.complexity module malva.compressed_index module malva.contrib module malva.datastore module malva.dbutils module malva.fast_map module malva.fastq_processing module malva.filter_minimizers module malva.index module malva.indexes module malva.kmer_processing module malva.quant module malva.reader module malva.search module malva.serve module malva.serve.modeling module malva.serve.reportgen module malva.serve.serve module malva.show module malva.spacemake module malva.utils module malva.xopen module malva_to_cellxmer() (in module malva.cellxmer) malva_to_filtered_cellxmer_chunked() (in module malva.cellxmer) MalvaIndex (class in malva.indexes) MalvaPlot (class in malva.show) MalvaProxyFix (class in malva.serve.serve) MalvaReferenceNotFound mask_low_complexity() (in module malva.complexity) merge_chunks() (malva.indexes.MalvaIndex method) module malva malva.autoannotate malva.cellxmer malva.cli malva.combine malva.complexity malva.compressed_index malva.contrib malva.datastore malva.dbutils malva.fast_map malva.fastq_processing malva.filter_minimizers malva.index malva.indexes malva.kmer_processing malva.quant malva.reader malva.search malva.serve malva.serve.modeling malva.serve.reportgen malva.serve.serve malva.show malva.spacemake malva.utils malva.xopen N n_chunks (malva.indexes.MalvaIndex attribute), [1] n_spatial (malva.indexes.MalvaIndex attribute) nonsingular() (in module malva.spacemake) num_buckets (malva.filter_minimizers.KmerFilter attribute), [1] num_items() (malva.indexes.SpatialIndex method) number_of_records (malva.fastq_processing.KmerFastqParser attribute) (malva.fastq_processing.SequenceFastqParser attribute) O open() (malva.indexes.MalvaIndex method) overlapping (malva.fastq_processing.FastKmerProcessor attribute) overlapping_windows() (in module malva.complexity) P PageAlignedArray (class in malva.datastore) PageCache (class in malva.datastore) parse_gene_lists() (in module malva.serve.modeling) parse_multifasta() (in module malva.dbutils) prefetch_chunks() (malva.compressed_index.CompressedArrayStorage method) preprocess_adata() (in module malva.autoannotate) process_batch() (in module malva.quant) process_dna_string() (in module malva.dbutils) process_ensembl_string() (in module malva.dbutils) process_gene_string() (in module malva.dbutils) process_group() (in module malva.combine) process_merge_chunks() (in module malva.combine) process_reference() (in module malva.quant) project_mapping (malva.indexes.MalvaIndex attribute) R read_sequences_file() (in module malva.search) resave_h5ad() (in module malva.quant) resize_dataset() (malva.datastore.ChunkedStore method) run_clustering() (in module malva.autoannotate) S safety_check_eval() (in module malva.utils) save() (malva.compressed_index.CompressedArrayStorage method) (malva.indexes.BackgroundModel method) save_binary() (malva.indexes.SpatialIndex method) save_index() (malva.dbutils.EnsemblLocalDB method) save_pickle() (in module malva.utils) scatter() (malva.show.MalvaPlot method) score_annotate() (in module malva.autoannotate) score_cells_by_cell_type() (in module malva.autoannotate) SequenceFastqParser (class in malva.fastq_processing) SequenceValidationError set_background_model() (malva.indexes.MalvaIndex method) set_barcode_index() (malva.indexes.MalvaIndex method) set_cache_size() (malva.compressed_index.CompressedArrayStorage method) set_spatial_coords() (malva.indexes.MalvaIndex method) set_spatial_index() (malva.indexes.MalvaIndex method) setup_autoannotate_parser() (in module malva.cli) setup_cellxmer_parser() (in module malva.cli) setup_combine_parser() (in module malva.cli) setup_index_parser() (in module malva.cli) setup_model() (in module malva.serve.modeling) setup_quant_parser() (in module malva.cli) setup_search_parser() (in module malva.cli) setup_serve_parser() (in module malva.cli) setup_show_parser() (in module malva.cli) shape (malva.compressed_index.CompressedArrayStorage property) (malva.datastore.PageAlignedArray attribute) simple_good_turing_smoothing() (in module malva.autoannotate) spatial_coord (malva.indexes.MalvaIndex attribute) SpatialData (class in malva.serve.serve) SpatialIndex (class in malva.indexes) submit_search_job() (in module malva.search) T total_mers (malva.indexes.BackgroundModel attribute) U umi_threshold_cell_calling() (in module malva.autoannotate) unload_chunks_from_memory() (malva.compressed_index.CompressedArrayStorage method) UserSession (class in malva.serve.serve) V validate_and_infer_query() (in module malva.dbutils) values (malva.serve.serve.SpatialData attribute) values() (malva.datastore.ChunkedStore method) verbose (malva.indexes.BackgroundModel attribute) (malva.indexes.MalvaIndex attribute), [1] W w (malva.filter_minimizers.KmerFilter attribute), [1] wait_for_completion() (in module malva.search) where() (malva.indexes.MalvaIndex method) write() (malva.indexes.MalvaIndex method) write_key_to_h5() (in module malva.utils) write_mtx_header() (in module malva.quant) X xmax (malva.serve.serve.SpatialData property) xmin (malva.serve.serve.SpatialData property) xopen() (in module malva.xopen) Y ymax (malva.serve.serve.SpatialData property) ymin (malva.serve.serve.SpatialData property)