Index

A

a_cluster (uchrom.strc.comp.axes_pc.CompartmentCallerParams attribute) (uchrom.strc.comp.CompartmentCallerParams attribute) accepted (uchrom_discovery.IdeaReview attribute) (uchrom_discovery.ideas.IdeaReview attribute) accepted_idea_target (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) add() (uchrom.core.intervals.IntervalStore method) (uchrom.core.zarrcd.SpotPartitionWriter method) add_annotation_features() (in module uchrom.fea) (in module uchrom.fea.annotation) add_canvas() (uchrom.browser.main_window.MainWindow method) add_canvas_hor() (uchrom.browser.main_window.MainWindow method) add_canvas_ver() (uchrom.browser.main_window.MainWindow method) add_edge() (uchrom_discovery.graph.IdeaGraph method) (uchrom_discovery.IdeaGraph method) add_node() (uchrom_discovery.graph.IdeaGraph method) (uchrom_discovery.IdeaGraph method) add_peak_features() (in module uchrom.fea) (in module uchrom.fea.peaks) add_reference() (uchrom.core.ChromData method) add_sequence_features() (in module uchrom.fea) (in module uchrom.fea.sequence) add_structural_features() (in module uchrom.strc.enrichment) add_user_annotation() (uchrom.core.ChromData method) add_widgets() (uchrom.browser.main_window.MainWindow method) adjust_camera() (uchrom.browser.main_window.MainWindow method) agent_name (uchrom_discovery.BackendAgentRecord attribute) (uchrom_discovery.backends.BackendAgentRecord attribute) (uchrom_discovery.pantheon.PantheonAgentRecord attribute) agent_records (uchrom_discovery.AnalysisCodeResult attribute) (uchrom_discovery.backends.AnalysisCodeResult attribute) agent_records_path (uchrom_discovery.DiscoveryRunResult attribute) (uchrom_discovery.runner.DiscoveryRunResult attribute) aggregate_over_tads() (in module uchrom.recon.fish._hic) aggregate_track_by_interval() (in module uchrom.fea) (in module uchrom.fea.peaks) aggregate_tracks() (in module uchrom.emb.cells) aggregate_tracks_by_interval() (in module uchrom.fea) (in module uchrom.fea.peaks)

align_embedding() (in module uchrom.emb.higashi) align_spots() (in module uchrom.im.trace), [1] align_substructure_to_scaffold() (in module uchrom.recon.bulk.mds.transforms) allow_reflection (uchrom.recon.fish._assembly.AssemblyParams attribute) allowed_required_fields() (in module uchrom_discovery) (in module uchrom_discovery.llm) alpha (uchrom.recon.fish._assembly.AssemblyParams attribute) analysis_code (uchrom_discovery.AnalysisCodeResult attribute) (uchrom_discovery.backends.AnalysisCodeResult attribute) analysis_output_schema() (in module uchrom_discovery) (in module uchrom_discovery.llm) analysis_plan (uchrom_discovery.DiscoveryIdea attribute) (uchrom_discovery.ideas.DiscoveryIdea attribute) AnalysisCodeResult (class in uchrom_discovery) (class in uchrom_discovery.backends) angle_weight (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) annotation_features (uchrom_discovery.DiscoveryEnrichmentConfig attribute) append_feature_registry_entry() (in module uchrom.fea) (in module uchrom.fea.registry) apply_distance_decay_prior() (in module uchrom.recon.bulk.mds) apply_transform() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.bulk.mds.transforms) array() (uchrom.core.zarrcd.Container method) artifact_manifest (uchrom_discovery.AnalysisCodeResult attribute) (uchrom_discovery.backends.AnalysisCodeResult attribute) assemble() (in module uchrom.recon.fish._assembly) AssemblyParams (class in uchrom.recon.fish._assembly) attempt (uchrom_discovery.pantheon.PantheonSchematicRecord attribute) auth_state (uchrom_discovery.BackendDetection attribute) (uchrom_discovery.backends.BackendDetection attribute) auto_discovery_schema (uchrom.core.ChromData property) available (uchrom_discovery.BackendDetection attribute) (uchrom_discovery.backends.BackendDetection attribute) axis_variance_cube() (in module uchrom.fea) (in module uchrom.fea.arc) axis_weight() (in module uchrom.fea) (in module uchrom.fea.arc)

B

backed (uchrom.core.backed.BackedChromData property) (uchrom.core.ChromData property) BackedArray (class in uchrom.core.backed) BackedChromData (class in uchrom.core.backed) BackedFrame (class in uchrom.core.backed) backend_id (uchrom_discovery.BackendDetection attribute) (uchrom_discovery.backends.BackendDetection attribute) (uchrom_discovery.backends.CLISpec attribute) (uchrom_discovery.backends.DiscoveryBackend attribute) (uchrom_discovery.backends.PantheonBackend attribute) (uchrom_discovery.CLISpec attribute) BackendAgentRecord (class in uchrom_discovery) (class in uchrom_discovery.backends) BackendCapabilities (class in uchrom_discovery) (class in uchrom_discovery.backends) BackendDetection (class in uchrom_discovery) (class in uchrom_discovery.backends) BackendError, [1] begin() (uchrom.core.zarrcd.SpotPartitionWriter method) bin_tracks (uchrom.core.ChromData property) bins (uchrom.core.ChromData property) bins_from_loci() (in module uchrom.core.bins)

biological_hypothesis (uchrom_discovery.DiscoveryIdea attribute) (uchrom_discovery.ideas.DiscoveryIdea attribute) bond_length (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) bond_log_probability() (in module uchrom.im.trace._polymer) bond_weight (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) build_analysis_prompt() (in module uchrom_discovery) (in module uchrom_discovery.llm) build_command (uchrom_discovery.backends.CLISpec attribute) (uchrom_discovery.CLISpec attribute) build_discovery_schema() (in module uchrom_discovery) (in module uchrom_discovery.schema) (uchrom.core.ChromData method) build_idea_graph_from_run() (in module uchrom_discovery) (in module uchrom_discovery.graph) build_idea_graph_from_runs() (in module uchrom_discovery) (in module uchrom_discovery.graph) build_idea_prompt() (in module uchrom_discovery) (in module uchrom_discovery.llm) build_required_fields_prompt_block() (in module uchrom_discovery) (in module uchrom_discovery.llm)

C

calc_di_batch() (in module uchrom.strc.tad.di) calc_directionality_index() (in module uchrom.strc.tad) (in module uchrom.strc.tad.di) call_compartments() (in module uchrom.tl) call_compartments_axes_pc() (in module uchrom.strc.comp) (in module uchrom.strc.comp.axes_pc) call_compartments_multi() (in module uchrom.strc.enrichment) call_domains_fishnet() (in module uchrom.strc.tad) (in module uchrom.strc.tad.fishnet) call_domains_fishnet_trace() (in module uchrom.strc.tad) (in module uchrom.strc.tad.fishnet) call_loops() (in module uchrom.tl) call_loops_axiswise_f() (in module uchrom.strc.loop) (in module uchrom.strc.loop.axiswise_f) call_loops_multi() (in module uchrom.strc.enrichment) call_macs_bdgpeaks_from_bedgraph() (in module uchrom.fea) (in module uchrom.fea.peaks) call_macs_bdgpeaks_from_signal() (in module uchrom.fea) (in module uchrom.fea.peaks) call_macs_peaks_from_signal() (in module uchrom.fea) (in module uchrom.fea.peaks) call_peaks_from_signal() (in module uchrom.fea) (in module uchrom.fea.peaks) call_peaks_from_track() (in module uchrom.fea) (in module uchrom.fea.peaks) call_structures_multi() (in module uchrom.strc.enrichment) call_tads() (in module uchrom.tl) call_tads_by_pval() (in module uchrom.strc.tad) (in module uchrom.strc.tad.arc_pval) call_tads_di() (in module uchrom.strc.tad) (in module uchrom.strc.tad.di_caller) call_tads_multi() (in module uchrom.strc.enrichment) capabilities() (uchrom_discovery.backends.CLIBackend method) (uchrom_discovery.backends.DiscoveryBackend method) (uchrom_discovery.backends.PantheonBackend method) capability_probe (uchrom_discovery.backends.CLISpec attribute) (uchrom_discovery.CLISpec attribute) cauchy_combination() (in module uchrom.utils) (in module uchrom.utils.stats) cell_positions() (uchrom.core.ChromData method) cell_shapes_geodataframe() (uchrom.core.ChromData method) cell_types (uchrom_discovery.DiscoveryIdea attribute) (uchrom_discovery.ideas.DiscoveryIdea attribute) center_coords() (in module uchrom.recon.bulk.mds.transforms) centre_gap_factor (uchrom.recon.fish._assembly.AssemblyParams attribute) change_current_canvas() (uchrom.browser.main_window.MainWindow method) ChromData (class in uchrom.core) chromdata (uchrom.core.UChromProject attribute), [1] chromdata_path (uchrom.core.UChromProject attribute), [1] chroms (uchrom.core.ChromData property) (uchrom_discovery.DiscoveryEnrichmentConfig attribute) claim_refresh_results (uchrom_discovery.iterative.IterativeDiscoveryResult attribute) (uchrom_discovery.IterativeDiscoveryResult attribute) ClaimRefreshResult (class in uchrom_discovery) claims_path (uchrom_discovery.ClaimRefreshResult attribute) claims_paths (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) classify_hypothesis_evidence() (in module uchrom_discovery) ClaudeBackend (class in uchrom_discovery.backends) clear_cache() (uchrom.core.zarrcd.SpotRows method) cli_flags (uchrom_discovery.BackendDetection attribute) (uchrom_discovery.backends.BackendDetection attribute)

CLIBackend (class in uchrom_discovery.backends) CLISpec (class in uchrom_discovery) (class in uchrom_discovery.backends) close() (uchrom.core.backed.BackedChromData method) (uchrom.core.zarrcd.Container method) cluster_cells() (in module uchrom.emb.cells) cmds_init() (in module uchrom.recon.bulk.mds.torch_mds) code_source (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) CodexBackend (class in uchrom_discovery.backends) coerce() (uchrom.core.intervals.IntervalStore class method) (uchrom.core.results.ResultsStore class method) columns (uchrom.core.backed.BackedFrame property) columns() (uchrom.core.zarrcd.SpotRows method) CompartmentCallerParams (class in uchrom.strc.comp) (class in uchrom.strc.comp.axes_pc) complexity (uchrom_discovery.DiscoveryIdea attribute) (uchrom_discovery.ideas.DiscoveryIdea attribute) computable_parameter (uchrom_discovery.DiscoveryIdea attribute) (uchrom_discovery.ideas.DiscoveryIdea attribute) compute_annotation_features() (in module uchrom.fea) (in module uchrom.fea.annotation) compute_distances() (uchrom.core.backed.BackedChromData method) (uchrom.core.ChromData method) compute_peak_features() (in module uchrom.fea) (in module uchrom.fea.peaks) compute_radius_of_gyration() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.bulk.mds.transforms) compute_sequence_features() (in module uchrom.fea) (in module uchrom.fea.sequence) compute_stress() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.bulk.mds.torch_mds) compute_structural_features() (in module uchrom.strc.enrichment) constraints (uchrom_discovery.DiscoveryDirection attribute) contact_frequency() (in module uchrom.fea) (in module uchrom.fea.distance) contact_to_distance() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.fish._hic) contacts_to_matrix() (in module uchrom.recon.bulk.mds) Container (class in uchrom.core.zarrcd) container_kind() (in module uchrom.core.zarrcd) content (uchrom_discovery.BackendAgentRecord attribute) (uchrom_discovery.backends.BackendAgentRecord attribute) (uchrom_discovery.pantheon.PantheonAgentRecord attribute) convergence_abs (uchrom.recon.fish._assembly.AssemblyParams attribute) convert() (in module uchrom.io.upgrade) coord_status() (uchrom.core.ChromData method) coords (uchrom.core.backed.BackedChromData property) coords_of() (uchrom.core.zarrcd.SpotRows method) copy() (uchrom.core.backed.BackedChromData method) (uchrom.core.ChromData method) create_contacts_from_cool() (in module uchrom.io) create_contacts_from_pairs() (in module uchrom.io) create_exploration_notebook() (in module uchrom_discovery) (in module uchrom_discovery.notebooks) create_particles_from_cool() (in module uchrom.io) create_particles_from_pairs() (in module uchrom.io) created_utc (uchrom.core.results.ResultRecord attribute), [1] cut_lo (uchrom.strc.loop.axiswise_f.LoopCallerParams attribute) (uchrom.strc.loop.LoopCallerParams attribute) cut_up (uchrom.strc.loop.axiswise_f.LoopCallerParams attribute) (uchrom.strc.loop.LoopCallerParams attribute)

D

dataset_name (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) dataset_references (uchrom.core.ChromData property) decode() (uchrom.core.zarrcd.SpotRows method) DEFAULT_CACHE_BYTES (in module uchrom.core.zarrcd) default_float_dtype() (in module uchrom.utils.stats) DEFAULT_ROW_GROUP_ROWS (in module uchrom.core.zarrcd) default_sigma_nm (uchrom.im.trace.SpotAlignerParams attribute), [1] default_target() (in module uchrom.io.upgrade) DEFAULT_ZSTD_LEVEL (in module uchrom.core.zarrcd) describe() (uchrom.core.UChromProject method), [1] describe_for_agent() (in module uchrom_discovery) (in module uchrom_discovery.schema) (uchrom.core.ChromData method) describe_links() (uchrom.core.ChromData method) detect() (uchrom_discovery.backends.CLIBackend method) (uchrom_discovery.backends.DiscoveryBackend method) (uchrom_discovery.backends.PantheonBackend method) detect_sisters (uchrom.im.trace.SpotAlignerParams attribute), [1] detect_tad_boundaries() (in module uchrom.strc.tad) (in module uchrom.strc.tad.di) device (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) (uchrom.recon.fish.GEMFISHParams attribute), [1] (uchrom_discovery.DiscoveryEnrichmentConfig attribute) DICallerParams (class in uchrom.strc.tad) (class in uchrom.strc.tad.di_caller) direction_context_path (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) direction_id (uchrom_discovery.DiscoveryDirection attribute) direction_status (uchrom_discovery.EvidenceConclusion attribute)

direction_summary_path (uchrom_discovery.DiscoveryRunResult attribute) (uchrom_discovery.iterative.IterativeDiscoveryResult attribute) (uchrom_discovery.IterativeDiscoveryResult attribute) (uchrom_discovery.runner.DiscoveryRunResult attribute) direction_type (uchrom_discovery.DiscoveryDirection attribute) directions_path (uchrom_discovery.DiscoveryRunResult attribute) (uchrom_discovery.iterative.IterativeDiscoveryResult attribute) (uchrom_discovery.IterativeDiscoveryResult attribute) (uchrom_discovery.runner.DiscoveryRunResult attribute) directions_to_agent_context() (in module uchrom_discovery) discovery_schema (uchrom.core.ChromData property) DiscoveryBackend (class in uchrom_discovery.backends) DiscoveryDirection (class in uchrom_discovery) DiscoveryEnrichmentConfig (class in uchrom_discovery) DiscoveryFrontier (in module uchrom_discovery) DiscoveryIdea (class in uchrom_discovery) (class in uchrom_discovery.ideas) DiscoveryRunConfig (class in uchrom_discovery) (class in uchrom_discovery.runner) DiscoveryRunResult (class in uchrom_discovery) (class in uchrom_discovery.runner) display_name (uchrom_discovery.backends.CLISpec attribute) (uchrom_discovery.backends.DiscoveryBackend attribute) (uchrom_discovery.backends.PantheonBackend attribute) (uchrom_discovery.CLISpec attribute) distance (uchrom.strc.tad.arc_pval.TADCallerParams attribute) (uchrom.strc.tad.TADCallerParams attribute) distance_map() (in module uchrom.fea) (in module uchrom.fea.distance) DistanceMap (class in uchrom.fea) (class in uchrom.fea.distance) downsample_coords() (in module uchrom.recon.bulk.mds.transforms) dtype (uchrom.core.backed.BackedArray attribute) dtypes (uchrom.core.backed.BackedFrame property)

E

edges (uchrom_discovery.graph.IdeaGraph attribute) (uchrom_discovery.IdeaGraph attribute) effect_size (uchrom_discovery.EvidenceConclusion attribute) embed_cells() (in module uchrom.emb.cells) EMBER_PROTOCOL (in module uchrom.recon.sc.ember) empty (uchrom.core.backed.BackedFrame property) empty() (uchrom.core.zarrcd.SpotRows method) empty_bins() (in module uchrom.core.bins) enabled() (uchrom_discovery.DiscoveryEnrichmentConfig method) encoding (uchrom.core.zarrcd.SpotRows attribute) end() (uchrom.core.zarrcd.SpotPartitionWriter method) endpoint_k (uchrom.recon.fish._assembly.AssemblyParams attribute) engine_info() (in module uchrom.recon.sc.nucdyn) enrich_for_discovery() (in module uchrom_discovery) enriched_h5cd_path (uchrom_discovery.DiscoveryRunResult attribute) (uchrom_discovery.runner.DiscoveryRunResult attribute) enrichment (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) enrichment_summary_path (uchrom_discovery.DiscoveryRunResult attribute) (uchrom_discovery.runner.DiscoveryRunResult attribute) error (uchrom_discovery.BackendDetection attribute) (uchrom_discovery.backends.BackendDetection attribute) (uchrom_discovery.pantheon.PantheonSchematicRecord attribute)

errors (uchrom_discovery.IdeaReview attribute) (uchrom_discovery.ideas.IdeaReview attribute) evidence_basis (uchrom_discovery.DiscoveryDirection attribute) EvidenceConclusion (class in uchrom_discovery) exclude_radius (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) exclude_weight (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) executable (uchrom_discovery.backends.CLISpec attribute) (uchrom_discovery.CLISpec attribute) executable_path (uchrom_discovery.BackendDetection attribute) (uchrom_discovery.backends.BackendDetection attribute) execute (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) execute_notebook_python() (in module uchrom_discovery) (in module uchrom_discovery.notebooks) exists() (uchrom.core.zarrcd.Container method) expected_direction (uchrom_discovery.DiscoveryIdea attribute) (uchrom_discovery.ideas.DiscoveryIdea attribute) expected_distance() (in module uchrom.im.trace._polymer) expected_distance_sq() (in module uchrom.im.trace._polymer) extra_cells (uchrom_discovery.AnalysisCodeResult attribute) (uchrom_discovery.backends.AnalysisCodeResult attribute) extract_structured_json() (in module uchrom_discovery.backends)

F

fallback_bins (uchrom_discovery.backends.CLISpec attribute) (uchrom_discovery.CLISpec attribute) fasta (uchrom_discovery.DiscoveryEnrichmentConfig attribute) fdr_cutoff (uchrom.strc.loop.axiswise_f.LoopCallerParams attribute) (uchrom.strc.loop.LoopCallerParams attribute) (uchrom.strc.tad.arc_pval.TADCallerParams attribute) (uchrom.strc.tad.TADCallerParams attribute) file_format_version() (in module uchrom.io.upgrade) file_sha256() (in module uchrom.fea.registry) file_workspace (uchrom_discovery.BackendCapabilities attribute) (uchrom_discovery.backends.BackendCapabilities attribute) files (uchrom.core.zarrcd.SpotRows attribute) fill_missing_distances() (in module uchrom.recon.bulk.mds) filter_contacts() (in module uchrom.io) filter_normalize() (in module uchrom.fea) (in module uchrom.fea.arc) fish_distance_loss() (in module uchrom.recon.fish._losses) FISHnetParams (class in uchrom.strc.tad) (class in uchrom.strc.tad.fishnet) fit_scale_factor() (in module uchrom.im.trace._polymer) fit_scale_factor_from_matrix() (in module uchrom.im.trace._polymer) format_version (uchrom.core.backed.BackedChromData property) frac (uchrom.strc.comp.axes_pc.CompartmentCallerParams attribute) (uchrom.strc.comp.CompartmentCallerParams attribute) (uchrom.strc.loop.axiswise_f.LoopCallerParams attribute) (uchrom.strc.loop.LoopCallerParams attribute) (uchrom.strc.tad.arc_pval.TADCallerParams attribute) (uchrom.strc.tad.TADCallerParams attribute)

from_chromdata() (uchrom.core.UChromProject class method), [1] from_dataframe() (uchrom.core.ChromData class method) from_dict() (uchrom_discovery.DiscoveryIdea class method) (uchrom_discovery.ideas.DiscoveryIdea class method) from_fofct() (uchrom.core.ChromData class method) from_frame() (uchrom.core.intervals.IntervalTable class method) from_pyhim_trace() (uchrom.core.ChromData class method) from_seqfish_multiomics() (uchrom.core.ChromData class method) from_seqfish_multiomics_linked() (uchrom.core.ChromData class method) from_takei2025_cerebellum() (uchrom.core.ChromData class method) frontier_context_path (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) frontier_id (uchrom_discovery.DiscoveryDirection property) frontier_summary_path (uchrom_discovery.DiscoveryRunResult property) (uchrom_discovery.iterative.IterativeDiscoveryResult property) (uchrom_discovery.IterativeDiscoveryResult property) (uchrom_discovery.runner.DiscoveryRunResult property) frontier_type (uchrom_discovery.DiscoveryDirection property) frontiers_path (uchrom_discovery.DiscoveryRunResult property) (uchrom_discovery.iterative.IterativeDiscoveryResult property) (uchrom_discovery.IterativeDiscoveryResult property) (uchrom_discovery.runner.DiscoveryRunResult property) frontiers_to_agent_context() (in module uchrom_discovery) (in module uchrom_discovery.frontier) function (uchrom.core.results.ResultRecord attribute), [1]

G

gap (uchrom.strc.loop.axiswise_f.LoopCallerParams attribute) (uchrom.strc.loop.LoopCallerParams attribute) gap_distance_from_contacts() (in module uchrom.recon.fish._assembly) gap_penalty (uchrom.im.trace.SpotAlignerParams attribute), [1] GEMFISHParams (class in uchrom.recon.fish), [1] generate_analysis_code() (uchrom_discovery.backends.CLIBackend method) (uchrom_discovery.backends.DiscoveryBackend method) (uchrom_discovery.backends.PantheonBackend method) generate_ideas() (uchrom_discovery.backends.CLIBackend method) (uchrom_discovery.backends.DiscoveryBackend method) (uchrom_discovery.backends.PantheonBackend method) generate_pantheon_ideas() (in module uchrom_discovery) (in module uchrom_discovery.pantheon) generate_pantheon_schematic_images_for_run() (in module uchrom_discovery.pantheon) generate_schematic_image (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) get() (uchrom_discovery.DiscoveryIdea method) (uchrom_discovery.ideas.DiscoveryIdea method) get_all_canvas() (uchrom.browser.main_window.MainWindow method) get_backend() (in module uchrom_discovery) (in module uchrom_discovery.backends) get_canvas_ix() (uchrom.browser.main_window.MainWindow method) get_cell() (uchrom.core.backed.BackedChromData method) (uchrom.core.ChromData method) get_cells() (uchrom.core.ChromData method) get_chrom() (uchrom.core.backed.BackedChromData method) (uchrom.core.ChromData method)

get_device() (in module uchrom.recon.bulk.mds.torch_mds) (in module uchrom.strc.tad.di) (in module uchrom.utils) (in module uchrom.utils.stats) get_discovery_schema() (in module uchrom_discovery) (in module uchrom_discovery.schema) get_domains() (in module uchrom.strc.tad) (in module uchrom.strc.tad.di) get_dtype() (in module uchrom.recon.bulk.mds.torch_mds) (in module uchrom.strc.tad.di) get_trace() (uchrom.core.backed.BackedChromData method) (uchrom.core.ChromData method) graph_html_path (uchrom_discovery.DiscoveryRunResult attribute) (uchrom_discovery.runner.DiscoveryRunResult attribute) graph_id (uchrom_discovery.graph.IdeaGraph attribute) (uchrom_discovery.IdeaGraph attribute) graph_path (uchrom_discovery.DiscoveryRunResult attribute) (uchrom_discovery.iterative.IterativeDiscoveryResult attribute) (uchrom_discovery.IterativeDiscoveryResult attribute) (uchrom_discovery.runner.DiscoveryRunResult attribute) graph_summary_markdown() (in module uchrom_discovery) (in module uchrom_discovery.graph) graph_summary_path (uchrom_discovery.DiscoveryRunResult attribute) (uchrom_discovery.iterative.IterativeDiscoveryResult attribute) (uchrom_discovery.IterativeDiscoveryResult attribute) (uchrom_discovery.runner.DiscoveryRunResult attribute) group_attrs() (uchrom.core.zarrcd.Container method) gtf (uchrom_discovery.DiscoveryEnrichmentConfig attribute)

H

h5cd_path (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) has_coords_table (uchrom.core.backed.BackedChromData property) hash_sources (uchrom_discovery.DiscoveryEnrichmentConfig attribute) head() (uchrom.core.backed.BackedFrame method) hic_alpha (uchrom.recon.fish.GEMFISHParams attribute), [1]

hic_fallback_beta (uchrom.recon.fish.GEMFISHParams attribute), [1] hic_fallback_c (uchrom.recon.fish.GEMFISHParams attribute), [1] hic_kl_loss() (in module uchrom.recon.fish._losses) hierarchical (uchrom.strc.tad.arc_pval.TADCallerParams attribute) (uchrom.strc.tad.TADCallerParams attribute) html_path (uchrom_discovery.iterative.IterativeDiscoveryResult attribute) (uchrom_discovery.IterativeDiscoveryResult attribute) hypothesis_status (uchrom_discovery.EvidenceConclusion attribute)

I

idea_agent_count (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) idea_id (uchrom_discovery.DiscoveryIdea attribute) (uchrom_discovery.ideas.DiscoveryIdea attribute) (uchrom_discovery.pantheon.PantheonSchematicRecord attribute) idea_markdown (uchrom_discovery.DiscoveryIdea attribute) (uchrom_discovery.ideas.DiscoveryIdea attribute) idea_output_schema() (in module uchrom_discovery) (in module uchrom_discovery.llm) idea_signature() (in module uchrom_discovery) (in module uchrom_discovery.graph) idea_source (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) idea_title (uchrom_discovery.DiscoveryIdea attribute) (uchrom_discovery.ideas.DiscoveryIdea attribute) idea_to_markdown() (in module uchrom_discovery) (in module uchrom_discovery.notebooks) IdeaGraph (class in uchrom_discovery) (class in uchrom_discovery.graph) IdeaReview (class in uchrom_discovery) (class in uchrom_discovery.ideas) ideas_path (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.DiscoveryRunResult attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) (uchrom_discovery.runner.DiscoveryRunResult attribute) ideas_per_iteration (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) iloc (uchrom.core.backed.BackedFrame property) image_path (uchrom_discovery.pantheon.PantheonSchematicRecord attribute) impute (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute)

impute() (in module uchrom.pp) index (uchrom.core.backed.BackedFrame property) index() (uchrom.core.zarrcd.SpotPartitionWriter method) infer_interval_kind() (in module uchrom.core.intervals) infer_kind() (in module uchrom.core.results) infer_parameter_family() (in module uchrom_discovery) (in module uchrom_discovery.graph) ingest_literature_claims() (in module uchrom_discovery) (in module uchrom_discovery.graph) init_draw() (uchrom.browser.main_window.MainWindow method) init_from_mds (uchrom.recon.fish._tad_level.Stage1Params attribute) init_scale (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) inner_cut (uchrom.strc.loop.axiswise_f.LoopCallerParams attribute) (uchrom.strc.loop.LoopCallerParams attribute) inner_max_iter (uchrom.recon.fish._assembly.AssemblyParams attribute) inputs (uchrom.core.results.ResultRecord attribute), [1] inter_mds() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.bulk.mds.inter) intervals (uchrom.core.ChromData property) IntervalStore (class in uchrom.core.intervals) IntervalTable (class in uchrom.core.intervals) is_coords (uchrom.core.zarrcd.SpotRows attribute) iter_cells() (uchrom.core.backed.BackedChromData method) (uchrom.core.ChromData method) iter_traces() (uchrom.core.backed.BackedChromData method) (uchrom.core.ChromData method) iteration_results (uchrom_discovery.iterative.IterativeDiscoveryResult attribute) (uchrom_discovery.IterativeDiscoveryResult attribute) iterations (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) iterative (uchrom.recon.fish._assembly.AssemblyParams attribute) IterativeDiscoveryConfig (class in uchrom_discovery) (class in uchrom_discovery.iterative) IterativeDiscoveryResult (class in uchrom_discovery) (class in uchrom_discovery.iterative)

K

k_sigma (uchrom.strc.comp.axes_pc.CompartmentCallerParams attribute) (uchrom.strc.comp.CompartmentCallerParams attribute) (uchrom.strc.loop.axiswise_f.LoopCallerParams attribute) (uchrom.strc.loop.LoopCallerParams attribute) (uchrom.strc.tad.arc_pval.TADCallerParams attribute) (uchrom.strc.tad.TADCallerParams attribute)

kind (uchrom.core.intervals.IntervalTable property) (uchrom.core.results.ResultRecord attribute), [1] knowledge_mode (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute)

L

lambda_E (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) lambda_E_intra (uchrom.recon.fish.GEMFISHParams attribute), [1] lambda_E_tad (uchrom.recon.fish.GEMFISHParams attribute), [1] lambda_F (uchrom.recon.fish._tad_level.Stage1Params attribute) (uchrom.recon.fish.GEMFISHParams attribute), [1] lambda_R (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish.GEMFISHParams attribute), [1] link_anndata() (uchrom.core.ChromData method) link_canvas (uchrom.browser.main_window.MainWindow property) link_cool() (uchrom.core.ChromData method) link_mudata() (uchrom.core.ChromData method) (uchrom.core.UChromProject method), [1] link_scool() (uchrom.core.ChromData method) (uchrom.core.UChromProject method), [1] link_spatialdata() (uchrom.core.ChromData method) (uchrom.core.UChromProject method), [1] linked_adata (uchrom.core.ChromData property) links (uchrom.core.UChromProject attribute), [1] list_backends() (in module uchrom_discovery) (in module uchrom_discovery.backends) llm_timeout (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute)

load_contact_matrix() (in module uchrom.recon.fish._hic) load_contacts() (in module uchrom.recon.sc.nucdyn) load_cool() (in module uchrom.io) load_idea_graph() (in module uchrom_discovery) (in module uchrom_discovery.graph) load_linked_anndata() (uchrom.core.ChromData method) load_linked_mudata() (uchrom.core.ChromData method) load_linked_scool() (uchrom.core.ChromData method) load_linked_spatialdata() (uchrom.core.ChromData method) load_model() (uchrom.browser.main_window.MainWindow method) load_mudata() (uchrom.core.UChromProject method), [1] load_scool() (uchrom.core.UChromProject method), [1] load_session_dialog() (uchrom.browser.main_window.MainWindow method) load_session_file() (uchrom.browser.main_window.MainWindow method) load_spatialdata() (uchrom.core.UChromProject method), [1] load_tad_from_bed() (in module uchrom.strc.tad) (in module uchrom.strc.tad.utils) loci_of() (in module uchrom.core.bins) LoopCallerParams (class in uchrom.strc.loop) (class in uchrom.strc.loop.axiswise_f) lowess_log_log() (in module uchrom.utils) (in module uchrom.utils.stats) lr (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute)

M

macs_bdgpeaks_to_narrowpeak() (in module uchrom.fea) (in module uchrom.fea.peaks) mahalanobis_cost() (in module uchrom.im.trace._polymer) main() (in module uchrom.io.upgrade) (in module uchrom.recon.sc.nucdyn) MainWindow (class in uchrom.browser.main_window) map_loci_to_bins() (in module uchrom.core.bins) marker_features() (in module uchrom.emb.cells) match_scales (uchrom.recon.fish._assembly.AssemblyParams attribute) max_bins_per_tad (uchrom.recon.fish._intra_tad.Stage2Params attribute) max_complexity (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) max_fibers_per_chrom (uchrom.im.trace.SpotAlignerParams attribute), [1] max_generation_attempts (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) max_ideas (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) max_levels (uchrom.strc.tad.arc_pval.TADCallerParams attribute) (uchrom.strc.tad.TADCallerParams attribute) max_skip (uchrom.im.trace.SpotAlignerParams attribute), [1] max_thresholds (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) mean_distance_matrix() (in module uchrom.fea) (in module uchrom.fea.distance) mean_edge_weight_cutoff (uchrom.im.trace.SpotAlignerParams attribute), [1] merge_substructures() (in module uchrom.strc.tad.utils) merge_tables() (in module uchrom.core.convention) merge_tol (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) metadata (uchrom_discovery.DiscoveryIdea attribute) (uchrom_discovery.ideas.DiscoveryIdea attribute) min_bins (uchrom.strc.comp.axes_pc.CompartmentCallerParams attribute) (uchrom.strc.comp.CompartmentCallerParams attribute) min_cluster_size (uchrom.strc.loop.axiswise_f.LoopCallerParams attribute) (uchrom.strc.loop.LoopCallerParams attribute) min_coverage (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) min_size_frac (uchrom.strc.tad.di_caller.DICallerParams attribute) (uchrom.strc.tad.DICallerParams attribute) min_spots_per_fiber (uchrom.im.trace.SpotAlignerParams attribute), [1] missing_fields (uchrom_discovery.IdeaReview attribute) (uchrom_discovery.ideas.IdeaReview attribute) modalities (uchrom_discovery.DiscoveryIdea attribute) (uchrom_discovery.ideas.DiscoveryIdea attribute) MODALITY_LABELS (in module uchrom.emb.cells) mode (uchrom_discovery.ClaimRefreshResult attribute) model (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) (uchrom_discovery.pantheon.PantheonSchematicRecord attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) module uchrom.browser uchrom.core uchrom.core.backed uchrom.core.bins uchrom.core.convention uchrom.core.intervals uchrom.core.results uchrom.core.zarrcd uchrom.emb.cells uchrom.emb.hic uchrom.emb.higashi uchrom.fea uchrom.fea.annotation uchrom.fea.arc uchrom.fea.distance uchrom.fea.peaks uchrom.fea.project uchrom.fea.registry uchrom.fea.sequence uchrom.im uchrom.im.trace uchrom.im.trace._polymer uchrom.io uchrom.io.upgrade uchrom.pl uchrom.pl.structure_3d uchrom.pl.trace_stats uchrom.pp uchrom.recon.bulk.mds uchrom.recon.bulk.mds.inter uchrom.recon.bulk.mds.torch_mds uchrom.recon.bulk.mds.transforms uchrom.recon.fish uchrom.recon.fish._assembly uchrom.recon.fish._hic uchrom.recon.fish._intra_tad uchrom.recon.fish._losses uchrom.recon.fish._tad_level uchrom.recon.sc.ember uchrom.recon.sc.gem uchrom.recon.sc.nucdyn uchrom.strc.comp uchrom.strc.enrichment uchrom.strc.loop uchrom.strc.tad uchrom.strc.tad.di uchrom.strc.tad.utils uchrom.tl uchrom.utils uchrom.utils.stats uchrom_discovery uchrom_discovery.backends uchrom_discovery.frontier uchrom_discovery.graph uchrom_discovery.ideas uchrom_discovery.iterative uchrom_discovery.llm uchrom_discovery.notebooks uchrom_discovery.pantheon uchrom_discovery.runner uchrom_discovery.schema uchrom_discovery.visualization

N

n_accepted (uchrom_discovery.DiscoveryRunResult attribute) (uchrom_discovery.runner.DiscoveryRunResult attribute) n_bins (uchrom.core.ChromData property) n_cells (uchrom.core.backed.BackedChromData property) (uchrom.core.ChromData property) n_claims (uchrom_discovery.ClaimRefreshResult attribute) n_clusters (uchrom.strc.comp.axes_pc.CompartmentCallerParams attribute) (uchrom.strc.comp.CompartmentCallerParams attribute) n_ensemble (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) n_executed (uchrom_discovery.DiscoveryRunResult attribute) (uchrom_discovery.runner.DiscoveryRunResult attribute) n_generated (uchrom_discovery.DiscoveryRunResult attribute) (uchrom_discovery.runner.DiscoveryRunResult attribute) n_iter (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) n_louvain_runs (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) n_partitions (uchrom.core.zarrcd.SpotRows property) n_spots (uchrom.core.backed.BackedChromData property) (uchrom.core.ChromData property) n_traces (uchrom.core.backed.BackedChromData property) (uchrom.core.ChromData property)

n_verified (uchrom_discovery.DiscoveryRunResult attribute) (uchrom_discovery.runner.DiscoveryRunResult attribute) native_available() (in module uchrom.recon.sc.nucdyn) native_skill_loading (uchrom_discovery.BackendCapabilities attribute) (uchrom_discovery.backends.BackendCapabilities attribute) ndim (uchrom.core.backed.BackedArray attribute) nodes (uchrom_discovery.graph.IdeaGraph attribute) (uchrom_discovery.IdeaGraph attribute) normalise_bins() (in module uchrom.core.bins) normalize_counts() (in module uchrom.emb.cells) normalize_distances() (in module uchrom.recon.bulk.mds) notebook (uchrom_discovery.pantheon.PantheonSchematicRecord attribute) notebook_agent_concurrency (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) notebook_status (uchrom_discovery.EvidenceConclusion attribute) notebooks (uchrom_discovery.DiscoveryRunResult attribute) (uchrom_discovery.runner.DiscoveryRunResult attribute) notes (uchrom_discovery.AnalysisCodeResult attribute) (uchrom_discovery.backends.AnalysisCodeResult attribute) (uchrom_discovery.ClaimRefreshResult attribute) novelty_notes (uchrom_discovery.DiscoveryDirection attribute)

O

on_click_canvas() (uchrom.browser.main_window.MainWindow method) on_toggle_show_axis() (uchrom.browser.main_window.MainWindow method) open_file_dialog() (uchrom.browser.main_window.MainWindow method) open_store_dialog() (uchrom.browser.main_window.MainWindow method) optimiser (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) outer_cut (uchrom.strc.loop.axiswise_f.LoopCallerParams attribute) (uchrom.strc.loop.LoopCallerParams attribute) outer_max_iter (uchrom.recon.fish._assembly.AssemblyParams attribute) output_dir (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.DiscoveryRunResult attribute) (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.iterative.IterativeDiscoveryResult attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryResult attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) (uchrom_discovery.runner.DiscoveryRunResult attribute)

overwrite (uchrom_discovery.DiscoveryEnrichmentConfig attribute) owns_notebook_lifecycle (uchrom_discovery.BackendCapabilities attribute) (uchrom_discovery.backends.BackendCapabilities attribute)

P

p_value (uchrom_discovery.EvidenceConclusion attribute) pack_schema() (in module uchrom_discovery) (in module uchrom_discovery.schema) PantheonAgentRecord (class in uchrom_discovery.pantheon) PantheonBackend (class in uchrom_discovery.backends) PantheonSchematicRecord (class in uchrom_discovery.pantheon) params (uchrom.core.results.ResultRecord attribute), [1] parent_idea_ids (uchrom_discovery.DiscoveryDirection attribute) parquet() (uchrom.core.zarrcd.Container method) parse_legacy_call() (in module uchrom.core.convention) part_chrom (uchrom.core.zarrcd.SpotPartitionWriter attribute) partition_dirs() (in module uchrom.core.zarrcd) partition_range() (uchrom.core.zarrcd.SpotRows method) partitioned (uchrom.core.backed.BackedChromData property) partitioned_mds() (in module uchrom.recon.bulk.mds) partitions (uchrom.core.zarrcd.SpotPartitionWriter attribute) peak_agg (uchrom_discovery.DiscoveryEnrichmentConfig attribute) peak_control_scale (uchrom_discovery.DiscoveryEnrichmentConfig attribute) peak_control_tracks (uchrom_discovery.DiscoveryEnrichmentConfig attribute) peak_cutoff (uchrom_discovery.DiscoveryEnrichmentConfig attribute) peak_fragment_size_bins (uchrom_discovery.DiscoveryEnrichmentConfig attribute) peak_genome_size (uchrom_discovery.DiscoveryEnrichmentConfig attribute) peak_large_local_window_bins (uchrom_discovery.DiscoveryEnrichmentConfig attribute) peak_max_gap (uchrom_discovery.DiscoveryEnrichmentConfig attribute) peak_max_gap_bins (uchrom_discovery.DiscoveryEnrichmentConfig attribute) peak_method (uchrom_discovery.DiscoveryEnrichmentConfig attribute) peak_min_length (uchrom_discovery.DiscoveryEnrichmentConfig attribute) peak_min_width_bins (uchrom_discovery.DiscoveryEnrichmentConfig attribute) peak_negative (uchrom_discovery.DiscoveryEnrichmentConfig attribute) peak_nolambda (uchrom_discovery.DiscoveryEnrichmentConfig attribute) peak_pvalue (uchrom_discovery.DiscoveryEnrichmentConfig attribute) peak_quantile (uchrom_discovery.DiscoveryEnrichmentConfig attribute) peak_qvalue (uchrom_discovery.DiscoveryEnrichmentConfig attribute) peak_signal_scale (uchrom_discovery.DiscoveryEnrichmentConfig attribute) peak_small_local_window_bins (uchrom_discovery.DiscoveryEnrichmentConfig attribute) peak_threshold (uchrom_discovery.DiscoveryEnrichmentConfig attribute) peak_tracks (uchrom_discovery.DiscoveryEnrichmentConfig attribute) persistence_length_bp (uchrom.im.trace.SpotAlignerParams attribute), [1] PERSISTENCE_LENGTH_BP_DEFAULT (in module uchrom.im.trace._polymer) pf() (uchrom.core.zarrcd.SpotRows method) physical() (uchrom.core.zarrcd.SpotRows method)

plain_columns (uchrom.core.zarrcd.SpotPartitionWriter attribute) plan_discovery_directions() (in module uchrom_discovery) plan_discovery_frontiers() (in module uchrom_discovery) (in module uchrom_discovery.frontier) plateau_size (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) plot_contact_map() (in module uchrom.pl) (in module uchrom.pl.trace_stats) plot_distance_matrix() (in module uchrom.pl) (in module uchrom.pl.trace_stats) plot_rg_histogram() (in module uchrom.pl) (in module uchrom.pl.trace_stats) plot_structure_3d() (in module uchrom.pl) (in module uchrom.pl.structure_3d) polymer_energy() (in module uchrom.recon.fish._losses) prefetch() (uchrom.core.zarrcd.Container method) prefix (uchrom.core.zarrcd.SpotPartitionWriter attribute) prior_graph_path (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) priority (uchrom_discovery.DiscoveryDirection attribute) procrustes_alignment() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.bulk.mds.transforms) project (uchrom_discovery.DiscoveryEnrichmentConfig attribute) project_existing_structure (uchrom_discovery.DiscoveryEnrichmentConfig attribute) project_interval_features_to_bins() (in module uchrom.fea) (in module uchrom.fea.project) project_interval_features_to_spots() (in module uchrom.fea) (in module uchrom.fea.project) prominence (uchrom.strc.tad.arc_pval.TADCallerParams attribute) (uchrom.strc.tad.TADCallerParams attribute) promoter_window (uchrom_discovery.DiscoveryEnrichmentConfig attribute) prompt (uchrom_discovery.DiscoveryDirection attribute) prompt_path (uchrom_discovery.BackendAgentRecord attribute) (uchrom_discovery.backends.BackendAgentRecord attribute) (uchrom_discovery.pantheon.PantheonAgentRecord attribute) (uchrom_discovery.pantheon.PantheonSchematicRecord attribute) prompt_via_stdin (uchrom_discovery.BackendCapabilities attribute) (uchrom_discovery.backends.BackendCapabilities attribute) provenance (uchrom.core.results.ResultRecord property) pval_cutoff (uchrom.strc.loop.axiswise_f.LoopCallerParams attribute) (uchrom.strc.loop.LoopCallerParams attribute)

R

radius_of_gyration() (in module uchrom.fea) (in module uchrom.fea.distance) random_state (uchrom.strc.comp.axes_pc.CompartmentCallerParams attribute) (uchrom.strc.comp.CompartmentCallerParams attribute) rationale (uchrom_discovery.DiscoveryDirection attribute) read() (uchrom.core.ChromData class method) read_all() (uchrom.core.zarrcd.SpotRows method) read_bedgraph() (in module uchrom.fea) (in module uchrom.fea.peaks) read_frame() (uchrom.core.zarrcd.Container method) read_gtf() (in module uchrom.fea) (in module uchrom.fea.annotation) read_pairs() (in module uchrom.io) read_particles() (in module uchrom.io) read_ranges() (uchrom.core.zarrcd.SpotRows method) read_small_parts() (in module uchrom.core.zarrcd) reasoning_effort (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) rebuild_bins() (uchrom.core.backed.BackedChromData method) (uchrom.core.ChromData method) reconstruct_ember() (in module uchrom.recon.sc.ember) reconstruct_gem_fish() (in module uchrom.recon.fish), [1] reconstruct_intra_tad() (in module uchrom.recon.fish._intra_tad) reconstruct_nucdyn() (in module uchrom.recon.sc.nucdyn) reconstruct_sc() (in module uchrom.tl) reconstruct_tad_level() (in module uchrom.recon.fish._tad_level) record() (uchrom.core.results.ResultsStore method) records() (uchrom.core.results.ResultsStore method) reflect_threshold (uchrom.recon.fish._assembly.AssemblyParams attribute) refresh_literature_claims_for_iteration() (in module uchrom_discovery) register_backend() (in module uchrom_discovery) (in module uchrom_discovery.backends) rel_path() (uchrom.core.zarrcd.SpotPartitionWriter method) remove_canvas() (uchrom.browser.main_window.MainWindow method) report_path (uchrom_discovery.DiscoveryRunResult attribute) (uchrom_discovery.runner.DiscoveryRunResult attribute)

required_fields (uchrom_discovery.DiscoveryIdea attribute) (uchrom_discovery.ideas.DiscoveryIdea attribute) resizeEvent() (uchrom.browser.main_window.MainWindow method) resolution (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) resolve_chroms() (in module uchrom.core.convention) resolve_link_path() (uchrom.core.ChromData method) ResultRecord (class in uchrom.core.results) results (uchrom.core.ChromData property) results_path (uchrom_discovery.DiscoveryRunResult attribute) (uchrom_discovery.runner.DiscoveryRunResult attribute) ResultsStore (class in uchrom.core.results) resume (uchrom_discovery.BackendCapabilities attribute) (uchrom_discovery.backends.BackendCapabilities attribute) retrieval_log_path (uchrom_discovery.ClaimRefreshResult attribute) review_idea_against_schema() (in module uchrom_discovery) (in module uchrom_discovery.ideas) reviews_path (uchrom_discovery.DiscoveryRunResult attribute) (uchrom_discovery.runner.DiscoveryRunResult attribute) rg_loss() (in module uchrom.recon.fish._losses) rg_squared() (in module uchrom.recon.fish._losses) role (uchrom_discovery.BackendAgentRecord attribute) (uchrom_discovery.backends.BackendAgentRecord attribute) (uchrom_discovery.pantheon.PantheonAgentRecord attribute) run() (in module uchrom.emb.higashi) run_auto_discovery() (in module uchrom_discovery) (in module uchrom_discovery.runner) run_dirs (uchrom_discovery.iterative.IterativeDiscoveryResult attribute) (uchrom_discovery.IterativeDiscoveryResult attribute) run_environment() (uchrom_discovery.backends.CLISpec method) (uchrom_discovery.CLISpec method) run_iterative_auto_discovery() (in module uchrom_discovery) (in module uchrom_discovery.iterative) run_mds() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.bulk.mds.torch_mds) run_pantheon_notebook_agents() (in module uchrom_discovery) (in module uchrom_discovery.pantheon)

S

save_particles() (in module uchrom.io) save_session() (uchrom.browser.main_window.MainWindow method) save_session_dialog() (uchrom.browser.main_window.MainWindow method) save_tads_to_bed() (in module uchrom.strc.tad.utils) scaling_exponent_fixed (uchrom.im.trace.SpotAlignerParams attribute), [1] schema_to_agent_context() (in module uchrom_discovery) (in module uchrom_discovery.schema) schematic_coverage_for_run() (in module uchrom_discovery) (in module uchrom_discovery.pantheon) schematic_image_model (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) schematic_image_model_args (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) schicluster_features() (in module uchrom.emb.hic) schicluster_impute() (in module uchrom.emb.hic) scool_cell_features() (in module uchrom.emb.hic) seed_run_dirs (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) select_spots() (in module uchrom.core.convention) selection_inputs() (in module uchrom.core.convention) sequence_features (uchrom_discovery.DiscoveryEnrichmentConfig attribute) set() (uchrom.core.results.ResultsStore method) set_cell_positions() (uchrom.core.ChromData method) (uchrom.core.UChromProject method), [1] set_cell_shapes() (uchrom.core.ChromData method) set_cell_spatial_coordinates() (uchrom.core.ChromData method) (uchrom.core.UChromProject method), [1] shape (uchrom.core.backed.BackedArray property) (uchrom.core.backed.BackedFrame property) sister_pair_radius_nm (uchrom.im.trace.SpotAlignerParams attribute), [1] size (uchrom.core.backed.BackedArray property) size_exclusion (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) smacof() (in module uchrom.recon.bulk.mds.torch_mds) smooth_with_moving_average() (in module uchrom.strc.tad.di) smoothing_param (uchrom.strc.tad.di_caller.DICallerParams attribute) (uchrom.strc.tad.DICallerParams attribute) sort_order() (in module uchrom.core.zarrcd) source_paths (uchrom_discovery.ClaimRefreshResult attribute)

source_result (uchrom.core.intervals.IntervalTable property) split_chrom (uchrom.core.zarrcd.SpotPartitionWriter attribute) split_spot_tracks() (in module uchrom.core.bins) spot_tracks (uchrom.core.backed.BackedChromData property) (uchrom.core.ChromData property) SpotAlignerParams (class in uchrom.im.trace), [1] SpotPartitionWriter (class in uchrom.core.zarrcd) SpotRows (class in uchrom.core.zarrcd) spots (uchrom.core.backed.BackedChromData property) spots_with_loci() (uchrom.core.backed.BackedChromData method) (uchrom.core.ChromData method) stable_idea_id() (in module uchrom_discovery.ideas) stage1_ensemble (uchrom.recon.fish.GEMFISHParams attribute), [1] stage1_iter (uchrom.recon.fish.GEMFISHParams attribute), [1] stage1_lr (uchrom.recon.fish.GEMFISHParams attribute), [1] stage1_optimiser (uchrom.recon.fish.GEMFISHParams attribute), [1] Stage1Params (class in uchrom.recon.fish._tad_level) stage2_ensemble (uchrom.recon.fish.GEMFISHParams attribute), [1] stage2_iter (uchrom.recon.fish.GEMFISHParams attribute), [1] stage2_lr (uchrom.recon.fish.GEMFISHParams attribute), [1] Stage2Params (class in uchrom.recon.fish._intra_tad) status (uchrom_discovery.pantheon.PantheonSchematicRecord attribute) stop_on_error (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) store_and_return() (in module uchrom.core.convention) store_discovery_schema() (in module uchrom_discovery) (in module uchrom_discovery.schema) store_schema (uchrom_discovery.DiscoveryRunConfig attribute) (uchrom_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom_discovery.IterativeDiscoveryConfig attribute) (uchrom_discovery.runner.DiscoveryRunConfig attribute) stream_format (uchrom_discovery.backends.CLISpec attribute) (uchrom_discovery.CLISpec attribute) streaming (uchrom_discovery.BackendCapabilities attribute) (uchrom_discovery.backends.BackendCapabilities attribute) structured_conclusion_markdown() (in module uchrom_discovery) structured_output (uchrom_discovery.BackendCapabilities attribute) (uchrom_discovery.backends.BackendCapabilities attribute) structures (uchrom_discovery.DiscoveryEnrichmentConfig attribute) substructures_from_tads() (in module uchrom.strc.tad) (in module uchrom.strc.tad.utils) summary (uchrom_discovery.EvidenceConclusion attribute) summary() (uchrom_discovery.graph.IdeaGraph method) (uchrom_discovery.IdeaGraph method)

T

table_provenance() (in module uchrom.fea.registry) tad_di_min_size_frac (uchrom.recon.fish.GEMFISHParams attribute), [1] tad_di_smoothing (uchrom.recon.fish.GEMFISHParams attribute), [1] tad_di_window (uchrom.recon.fish.GEMFISHParams attribute), [1] tad_max_size_frac (uchrom.recon.fish.GEMFISHParams attribute), [1] tad_regions_to_bin_indices() (in module uchrom.strc.tad.utils) TADCallerParams (class in uchrom.strc.tad) (class in uchrom.strc.tad.arc_pval) take() (uchrom.core.zarrcd.SpotRows method) target_facets (uchrom_discovery.DiscoveryDirection attribute) tau_nm_per_bp (uchrom.im.trace.SpotAlignerParams attribute), [1] tfidf_lsi() (in module uchrom.emb.cells) threshold_max (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) threshold_min (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) threshold_step (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) thresholds (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) title (uchrom_discovery.DiscoveryDirection attribute) to_anndata() (uchrom.core.backed.BackedChromData method) (uchrom.core.ChromData method) to_bins() (uchrom.core.intervals.IntervalStore method) (uchrom.core.intervals.IntervalTable method) to_dataframe() (uchrom.core.backed.BackedChromData method) (uchrom.core.ChromData method)

to_dict() (uchrom.core.results.ResultsStore method) (uchrom_discovery.ClaimRefreshResult method) (uchrom_discovery.DiscoveryDirection method) (uchrom_discovery.DiscoveryIdea method) (uchrom_discovery.graph.IdeaGraph method) (uchrom_discovery.IdeaGraph method) (uchrom_discovery.IdeaReview method) (uchrom_discovery.ideas.DiscoveryIdea method) (uchrom_discovery.ideas.IdeaReview method) (uchrom_discovery.iterative.IterativeDiscoveryResult method) (uchrom_discovery.IterativeDiscoveryResult method) to_fofct() (uchrom.core.ChromData method) to_frame() (uchrom.core.zarrcd.SpotRows method) to_memory() (uchrom.core.backed.BackedChromData method) (uchrom.core.ChromData method) to_numpy() (uchrom.core.backed.BackedArray method) to_pandas() (uchrom.core.backed.BackedFrame method) to_spatialdata() (uchrom.core.ChromData method) torch_mds() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.bulk.mds.torch_mds) track_names() (uchrom.core.ChromData method) tracks (uchrom.core.ChromData property) tracks_spot_view() (uchrom.core.backed.BackedChromData method) (uchrom.core.ChromData method) trigger_other_canvas_mouse_event() (uchrom.browser.main_window.MainWindow method)

U

uchrom.browser module uchrom.core module uchrom.core.backed module uchrom.core.bins module uchrom.core.convention module uchrom.core.intervals module uchrom.core.results module uchrom.core.zarrcd module uchrom.emb.cells module uchrom.emb.hic module uchrom.emb.higashi module uchrom.fea module uchrom.fea.annotation module uchrom.fea.arc module uchrom.fea.distance module uchrom.fea.peaks module uchrom.fea.project module uchrom.fea.registry module uchrom.fea.sequence module uchrom.im module uchrom.im.trace module uchrom.im.trace._polymer module uchrom.io module uchrom.io.upgrade module uchrom.pl module uchrom.pl.structure_3d module uchrom.pl.trace_stats module uchrom.pp module uchrom.recon.bulk.mds module uchrom.recon.bulk.mds.inter module uchrom.recon.bulk.mds.torch_mds module uchrom.recon.bulk.mds.transforms module uchrom.recon.fish module uchrom.recon.fish._assembly module uchrom.recon.fish._hic module

uchrom.recon.fish._intra_tad module uchrom.recon.fish._losses module uchrom.recon.fish._tad_level module uchrom.recon.sc.ember module uchrom.recon.sc.gem module uchrom.recon.sc.nucdyn module uchrom.strc.comp module uchrom.strc.enrichment module uchrom.strc.loop module uchrom.strc.tad module uchrom.strc.tad.di module uchrom.strc.tad.utils module uchrom.tl module uchrom.utils module uchrom.utils.stats module uchrom_discovery module uchrom_discovery.backends module uchrom_discovery.frontier module uchrom_discovery.graph module uchrom_discovery.ideas module uchrom_discovery.iterative module uchrom_discovery.llm module uchrom_discovery.notebooks module uchrom_discovery.pantheon module uchrom_discovery.runner module uchrom_discovery.schema module uchrom_discovery.visualization module uchrom_version (uchrom.core.results.ResultRecord attribute), [1] UChromProject (class in uchrom.core), [1] unique_spot_intervals() (in module uchrom.fea) (in module uchrom.fea.project) unpack_schema() (in module uchrom_discovery) (in module uchrom_discovery.schema) unregister_backend() (in module uchrom_discovery) (in module uchrom_discovery.backends) UNSET (in module uchrom.core.convention) update_canvas_border_color() (uchrom.browser.main_window.MainWindow method) update_discovery_schema() (uchrom.core.ChromData method) upgrade_h5cd() (in module uchrom.io.upgrade) upsert_structured_conclusion() (in module uchrom_discovery) (in module uchrom_discovery.notebooks) user_annotations (uchrom.core.ChromData property)

V

validate() (uchrom.core.UChromProject method), [1] validate_discovery_schema() (in module uchrom_discovery) (in module uchrom_discovery.schema) (uchrom.core.ChromData method) validate_intervals() (in module uchrom.core.intervals) validate_links() (uchrom.core.ChromData method) validate_value() (in module uchrom.core.results) validation_checks (uchrom_discovery.DiscoveryIdea attribute) (uchrom_discovery.ideas.DiscoveryIdea attribute)

value (uchrom.core.results.ResultRecord attribute), [1] verbose (uchrom.im.trace.SpotAlignerParams attribute), [1] (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) (uchrom.recon.fish.GEMFISHParams attribute), [1] (uchrom_discovery.DiscoveryEnrichmentConfig attribute) version (uchrom_discovery.BackendDetection attribute) (uchrom_discovery.backends.BackendDetection attribute) visual_qa (uchrom_discovery.pantheon.PantheonSchematicRecord attribute)

W

warnings (uchrom_discovery.AnalysisCodeResult attribute) (uchrom_discovery.backends.AnalysisCodeResult attribute) (uchrom_discovery.IdeaReview attribute) (uchrom_discovery.ideas.IdeaReview attribute) window (uchrom.strc.tad.di_caller.DICallerParams attribute) (uchrom.strc.tad.DICallerParams attribute) window_bp (uchrom.strc.tad.arc_pval.TADCallerParams attribute) (uchrom.strc.tad.TADCallerParams attribute) window_size (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) write() (uchrom.core.backed.BackedChromData method) (uchrom.core.ChromData method) write_direction_artifacts() (in module uchrom_discovery)

write_empty() (uchrom.core.zarrcd.SpotPartitionWriter method) write_frontier_artifacts() (in module uchrom_discovery) (in module uchrom_discovery.frontier) write_idea_graph_artifacts() (in module uchrom_discovery) (in module uchrom_discovery.graph) write_idea_graph_html() (in module uchrom_discovery) (in module uchrom_discovery.visualization) write_json() (uchrom_discovery.graph.IdeaGraph method) (uchrom_discovery.IdeaGraph method) write_summary_markdown() (uchrom_discovery.graph.IdeaGraph method) (uchrom_discovery.IdeaGraph method) write_zarr() (in module uchrom.core.zarrcd) writer() (uchrom.core.ChromData class method)

Z

ZARR_LAYOUT_VERSION (in module uchrom.core.zarrcd)

ZARR_LAYOUTS (in module uchrom.core.zarrcd)