Index A | B | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | U | V | W | X A add_dataset_member() (sc_tools.registry.Registry method) add_patient() (sc_tools.registry.Registry method) add_project() (sc_tools.registry.Registry method) add_subject() (sc_tools.registry.Registry method) aggressive_cleanup() (in module sc_tools.memory) annotation_colors_from_categories() (in module sc_tools.pl.heatmaps) apply_qc_filter() (in module sc_tools.qc) arcsinh_transform() (in module sc_tools.pp) B backup_raw() (in module sc_tools.pp) branch (sc_tools.pipeline.PhaseSpec attribute) build_sbatch_header() (in module sc_tools.ingest.slurm) bump_dataset_version() (sc_tools.registry.Registry method) C calculate_qc_metrics() (in module sc_tools.qc) check_gpu_available() (in module sc_tools.memory) check_memory_threshold() (in module sc_tools.memory) checkpoint (sc_tools.pipeline.PhaseSpec attribute) CheckpointValidationError (class in sc_tools.validate) classify_samples() (in module sc_tools.qc) clean_sig_name() (in module sc_tools.utils) cluster() (in module sc_tools.pp) cluster_within_groups() (in module sc_tools.pl.heatmaps) collect_all_batches() (in module sc_tools.ingest.config) compare_integrations() (in module sc_tools.bm.integration) compute_composite_score() (in module sc_tools.bm.integration) compute_integration_metrics() (in module sc_tools.bm.integration) compute_sample_metrics() (in module sc_tools.qc) compute_segmentation_accuracy() (in module sc_tools.bm.segmentation) concat_samples() (in module sc_tools.ingest.loaders) create_dataset() (sc_tools.registry.Registry method) D deconvolution() (in module sc_tools.tl) delete_project() (sc_tools.registry.Registry method) depends_on (sc_tools.pipeline.PhaseSpec attribute) E estimate_adata_memory() (in module sc_tools.memory) extend_dag() (in module sc_tools.pipeline) extract_reference_profiles() (in module sc_tools.tl) F filter_cells() (in module sc_tools.qc) filter_genes() (in module sc_tools.qc) filter_genes_by_pattern() (in module sc_tools.pp) filter_signatures() (in module sc_tools.utils) filter_spots() (in module sc_tools.qc) G generate_all_qc_reports() (in module sc_tools.qc) generate_post_celltyping_report() (in module sc_tools.qc) generate_post_filter_report() (in module sc_tools.qc) generate_post_integration_report() (in module sc_tools.qc) generate_pre_filter_report() (in module sc_tools.qc) generate_qc_report() (in module sc_tools.qc) generate_segmentation_qc_report() (in module sc_tools.qc) get_available_next() (in module sc_tools.pipeline) get_biodata() (sc_tools.registry.Registry method) get_dag() (in module sc_tools.pipeline) get_data_source() (sc_tools.registry.Registry method) get_dataset() (sc_tools.registry.Registry method) get_dataset_members() (sc_tools.registry.Registry method) get_dataset_uri() (sc_tools.registry.Registry method) get_inventory_item() (sc_tools.registry.Registry method) get_memory_usage() (in module sc_tools.memory) get_obs_category_colors() (in module sc_tools.pl.heatmaps) get_patient() (sc_tools.registry.Registry method) get_phase() (in module sc_tools.pipeline) (sc_tools.registry.Registry method) get_phase_checkpoint() (in module sc_tools.pipeline) get_project() (sc_tools.registry.Registry method) get_provenance() (sc_tools.registry.Registry method) get_sample() (sc_tools.registry.Registry method) get_signature_columns() (in module sc_tools.utils) get_subject() (sc_tools.registry.Registry method) get_version_prefix() (in module sc_tools.utils) H highly_variable_genes() (in module sc_tools.qc) human_in_loop (sc_tools.pipeline.PhaseSpec attribute) I iterative (sc_tools.pipeline.PhaseSpec attribute) L label (sc_tools.pipeline.PhaseSpec attribute) leiden() (in module sc_tools.pp) link_project_data_source() (sc_tools.registry.Registry method) link_project_dataset() (sc_tools.registry.Registry method) list_biodata() (sc_tools.registry.Registry method) list_data_sources() (sc_tools.registry.Registry method) list_datasets() (sc_tools.registry.Registry method) list_gene_sets() (in module sc_tools.tl) list_inventory_items() (sc_tools.registry.Registry method) list_patients() (sc_tools.registry.Registry method) list_phases() (sc_tools.registry.Registry method) list_project_data_sources() (sc_tools.registry.Registry method) list_project_datasets() (sc_tools.registry.Registry method) list_projects() (sc_tools.registry.Registry method) list_samples() (sc_tools.registry.Registry method) list_subjects() (sc_tools.registry.Registry method) load_batch_manifest() (in module sc_tools.ingest.config) load_cellpose_mask() (in module sc_tools.bm.mask_io) load_cellprofiler_mask() (in module sc_tools.bm.mask_io) load_deepcell_mask() (in module sc_tools.bm.mask_io) load_gmt() (in module sc_tools.tl) load_hallmark() (in module sc_tools.tl) load_he_image() (in module sc_tools.ingest.loaders) load_imc_sample() (in module sc_tools.ingest.loaders) load_mask() (in module sc_tools.bm.mask_io) load_msigdb_json() (in module sc_tools.tl) load_stardist_mask() (in module sc_tools.bm.mask_io) load_tiff_mask() (in module sc_tools.bm.mask_io) load_visium_hd_cell_sample() (in module sc_tools.ingest.loaders) load_visium_hd_sample() (in module sc_tools.ingest.loaders) load_visium_sample() (in module sc_tools.ingest.loaders) load_xenium_sample() (in module sc_tools.ingest.loaders) log_memory() (in module sc_tools.memory) log_transform() (in module sc_tools.pp) M mark_phase_complete() (sc_tools.registry.Registry method) merge_gene_signatures() (in module sc_tools.tl) morans_i() (in module sc_tools.tl.colocalization) morans_i_batch() (in module sc_tools.tl.colocalization) multipage_spatial_pdf() (in module sc_tools.pl.spatial) N neighborhood_enrichment() (in module sc_tools.tl.colocalization) neighborhood_enrichment_batch() (in module sc_tools.tl.colocalization) neighbors() (in module sc_tools.pp) normalize_total() (in module sc_tools.pp) O old_code (sc_tools.pipeline.PhaseSpec attribute) open_file() (in module sc_tools.storage) optional (sc_tools.pipeline.PhaseSpec attribute) P pca() (in module sc_tools.pp) pearson_correlation() (in module sc_tools.tl.colocalization) phase_group (sc_tools.pipeline.PhaseSpec attribute) PhaseSpec (class in sc_tools.pipeline) plot_gsea_dotplot() (in module sc_tools.pl) plot_highly_variable_genes() (in module sc_tools.pl) (in module sc_tools.qc.plots) plot_spatial_categorical() (in module sc_tools.pl.spatial) plot_spatial_continuous() (in module sc_tools.pl.spatial) plot_spatial_plain_he() (in module sc_tools.pl.spatial) plot_spatially_variable_genes() (in module sc_tools.pl) (in module sc_tools.qc.plots) preprocess() (in module sc_tools.pp) project_data_summary() (sc_tools.registry.Registry method) Q qc_2x2_grid() (in module sc_tools.pl) (in module sc_tools.qc.plots) qc_2x4_pre_post() (in module sc_tools.pl) (in module sc_tools.qc.plots) qc_report (sc_tools.pipeline.PhaseSpec attribute) qc_sample_comparison_bar() (in module sc_tools.pl) (in module sc_tools.qc.plots) qc_sample_scatter_matrix() (in module sc_tools.pl) (in module sc_tools.qc.plots) qc_sample_violin_grouped() (in module sc_tools.pl) (in module sc_tools.qc.plots) qc_scatter_counts_genes() (in module sc_tools.pl) (in module sc_tools.qc.plots) qc_spatial_multipage() (in module sc_tools.pl) (in module sc_tools.qc.plots) qc_violin_metrics() (in module sc_tools.pl) (in module sc_tools.qc.plots) R record_provenance() (sc_tools.registry.Registry method) register_biodata() (sc_tools.registry.Registry method) register_data() (sc_tools.registry.Registry method) register_data_source() (sc_tools.registry.Registry method) register_dataset() (sc_tools.registry.Registry method) register_inventory_item() (sc_tools.registry.Registry method) register_sample() (sc_tools.registry.Registry method) Registry (class in sc_tools.registry) remove_dataset_member() (sc_tools.registry.Registry method) required_obs (sc_tools.pipeline.PhaseSpec attribute) required_obsm (sc_tools.pipeline.PhaseSpec attribute) resolve_fs() (in module sc_tools.storage) run_bbknn() (in module sc_tools.pp) run_cellpose() (in module sc_tools.bm.segment) run_combat() (in module sc_tools.pp) run_cytovi() (in module sc_tools.pp) run_deepcell() (in module sc_tools.bm.segment) run_full_integration_workflow() (in module sc_tools.bm.integration) run_gsea_pseudobulk() (in module sc_tools.tl) run_harmony() (in module sc_tools.pp) run_imc_phenotyping() (in module sc_tools.pp.integrate) run_integration_benchmark() (in module sc_tools.bm.integration) run_ora() (in module sc_tools.tl) run_scanorama() (in module sc_tools.pp) run_scanvi() (in module sc_tools.pp) run_scvi() (in module sc_tools.pp) run_stardist() (in module sc_tools.bm.segment) run_utag() (in module sc_tools.pp) S save_figure() (in module sc_tools.pl) save_gene_signatures() (in module sc_tools.tl) save_pass_fail_lists() (in module sc_tools.qc) scale() (in module sc_tools.pp) score_segmentation() (in module sc_tools.bm.segmentation) score_signature() (in module sc_tools.tl) select_signature_genes() (in module sc_tools.tl) signature_score_heatmap() (in module sc_tools.pl.heatmaps) smart_read_csv() (in module sc_tools.storage) smart_read_h5ad() (in module sc_tools.storage) smart_write_checkpoint() (in module sc_tools.storage) spatially_variable_genes() (in module sc_tools.qc) spatially_variable_genes_per_library() (in module sc_tools.qc) status() (sc_tools.registry.Registry method) T truncated_similarity() (in module sc_tools.tl.colocalization) U umap() (in module sc_tools.pp) update_dataset_status() (sc_tools.registry.Registry method) update_gene_symbols() (in module sc_tools.tl) upsert_phase() (sc_tools.registry.Registry method) V validate_checkpoint() (in module sc_tools.validate) validate_dag() (in module sc_tools.pipeline) validate_file() (in module sc_tools.validate) validate_gene_signatures() (in module sc_tools.tl) validate_manifest() (in module sc_tools.ingest.config) validate_p1() (in module sc_tools.validate) validate_p2() (in module sc_tools.validate) validate_p3() (in module sc_tools.validate) validate_p35() (in module sc_tools.validate) validate_p4() (in module sc_tools.validate) versioned_filename() (in module sc_tools.utils) versioned_path() (in module sc_tools.utils) W with_local_copy() (in module sc_tools.storage) write_sbatch_script() (in module sc_tools.ingest.slurm) X x_format (sc_tools.pipeline.PhaseSpec attribute)