Index

A

a_cluster (uchrom.strc.comp.axes_pc.CompartmentCallerParams attribute) (uchrom.strc.comp.CompartmentCallerParams attribute) accepted (uchrom.auto_discovery.IdeaReview attribute) (uchrom.auto_discovery.ideas.IdeaReview attribute) accepted_idea_target (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) 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.auto_discovery.graph.IdeaGraph method) (uchrom.auto_discovery.IdeaGraph method) add_node() (uchrom.auto_discovery.graph.IdeaGraph method) (uchrom.auto_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.auto_discovery.BackendAgentRecord attribute) (uchrom.auto_discovery.backends.BackendAgentRecord attribute) (uchrom.auto_discovery.pantheon.PantheonAgentRecord attribute) agent_records (uchrom.auto_discovery.AnalysisCodeResult attribute) (uchrom.auto_discovery.backends.AnalysisCodeResult attribute) agent_records_path (uchrom.auto_discovery.DiscoveryRunResult attribute) (uchrom.auto_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_by_interval() (in module uchrom.fea) (in module uchrom.fea.peaks)

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.auto_discovery) (in module uchrom.auto_discovery.llm) alpha (uchrom.recon.fish._assembly.AssemblyParams attribute) analysis_code (uchrom.auto_discovery.AnalysisCodeResult attribute) (uchrom.auto_discovery.backends.AnalysisCodeResult attribute) analysis_output_schema() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.llm) analysis_plan (uchrom.auto_discovery.DiscoveryIdea attribute) (uchrom.auto_discovery.ideas.DiscoveryIdea attribute) AnalysisCodeResult (class in uchrom.auto_discovery) (class in uchrom.auto_discovery.backends) angle_weight (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) annotation_features (uchrom.auto_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) artifact_manifest (uchrom.auto_discovery.AnalysisCodeResult attribute) (uchrom.auto_discovery.backends.AnalysisCodeResult attribute) assemble() (in module uchrom.recon.fish._assembly) AssemblyParams (class in uchrom.recon.fish._assembly) attempt (uchrom.auto_discovery.pantheon.PantheonSchematicRecord attribute) auth_state (uchrom.auto_discovery.BackendDetection attribute) (uchrom.auto_discovery.backends.BackendDetection attribute) auto_discovery_schema (uchrom.core.ChromData property) available (uchrom.auto_discovery.BackendDetection attribute) (uchrom.auto_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

backend_id (uchrom.auto_discovery.BackendDetection attribute) (uchrom.auto_discovery.backends.BackendDetection attribute) (uchrom.auto_discovery.backends.CLISpec attribute) (uchrom.auto_discovery.backends.DiscoveryBackend attribute) (uchrom.auto_discovery.backends.PantheonBackend attribute) (uchrom.auto_discovery.CLISpec attribute) BackendAgentRecord (class in uchrom.auto_discovery) (class in uchrom.auto_discovery.backends) BackendCapabilities (class in uchrom.auto_discovery) (class in uchrom.auto_discovery.backends) BackendDetection (class in uchrom.auto_discovery) (class in uchrom.auto_discovery.backends) BackendError, [1] biological_hypothesis (uchrom.auto_discovery.DiscoveryIdea attribute) (uchrom.auto_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.auto_discovery) (in module uchrom.auto_discovery.llm) build_command (uchrom.auto_discovery.backends.CLISpec attribute) (uchrom.auto_discovery.CLISpec attribute) build_discovery_schema() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.schema) (uchrom.core.ChromData method) build_idea_graph_from_run() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.graph) build_idea_graph_from_runs() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.graph) build_idea_prompt() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.llm) build_required_fields_prompt_block() (in module uchrom.auto_discovery) (in module uchrom.auto_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_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_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_by_pval() (in module uchrom.strc.tad) (in module uchrom.strc.tad.arc_pval) call_tads_multi() (in module uchrom.strc.enrichment) capabilities() (uchrom.auto_discovery.backends.CLIBackend method) (uchrom.auto_discovery.backends.DiscoveryBackend method) (uchrom.auto_discovery.backends.PantheonBackend method) capability_probe (uchrom.auto_discovery.backends.CLISpec attribute) (uchrom.auto_discovery.CLISpec attribute) cauchy_combination() (in module uchrom.utils) (in module uchrom.utils.stats) cell_types (uchrom.auto_discovery.DiscoveryIdea attribute) (uchrom.auto_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) chroms (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) (uchrom.core.ChromData property) claim_refresh_results (uchrom.auto_discovery.iterative.IterativeDiscoveryResult attribute) (uchrom.auto_discovery.IterativeDiscoveryResult attribute) ClaimRefreshResult (class in uchrom.auto_discovery) claims_path (uchrom.auto_discovery.ClaimRefreshResult attribute) claims_paths (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) classify_hypothesis_evidence() (in module uchrom.auto_discovery)

ClaudeBackend (class in uchrom.auto_discovery.backends) cli_flags (uchrom.auto_discovery.BackendDetection attribute) (uchrom.auto_discovery.backends.BackendDetection attribute) CLIBackend (class in uchrom.auto_discovery.backends) CLISpec (class in uchrom.auto_discovery) (class in uchrom.auto_discovery.backends) cmds_init() (in module uchrom.recon.bulk.mds.torch_mds) code_source (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) CodexBackend (class in uchrom.auto_discovery.backends) CompartmentCallerParams (class in uchrom.strc.comp) (class in uchrom.strc.comp.axes_pc) complexity (uchrom.auto_discovery.DiscoveryIdea attribute) (uchrom.auto_discovery.ideas.DiscoveryIdea attribute) computable_parameter (uchrom.auto_discovery.DiscoveryIdea attribute) (uchrom.auto_discovery.ideas.DiscoveryIdea attribute) compute_annotation_features() (in module uchrom.fea) (in module uchrom.fea.annotation) compute_distances() (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.auto_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) content (uchrom.auto_discovery.BackendAgentRecord attribute) (uchrom.auto_discovery.backends.BackendAgentRecord attribute) (uchrom.auto_discovery.pantheon.PantheonAgentRecord attribute) convergence_abs (uchrom.recon.fish._assembly.AssemblyParams attribute) copy() (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.auto_discovery) (in module uchrom.auto_discovery.notebooks) create_particles_from_cool() (in module uchrom.io) create_particles_from_pairs() (in module uchrom.io) 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.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) dataset_references (uchrom.core.ChromData property) default_float_dtype() (in module uchrom.utils.stats) default_sigma_nm (uchrom.im.trace.SpotAlignerParams attribute), [1] describe_for_agent() (uchrom.core.ChromData method) detect() (uchrom.auto_discovery.backends.CLIBackend method) (uchrom.auto_discovery.backends.DiscoveryBackend method) (uchrom.auto_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.auto_discovery.DiscoveryEnrichmentConfig attribute) (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) (uchrom.recon.fish.GEMFISHParams attribute), [1] direction_context_path (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) direction_id (uchrom.auto_discovery.DiscoveryDirection attribute) direction_status (uchrom.auto_discovery.EvidenceConclusion attribute) direction_summary_path (uchrom.auto_discovery.DiscoveryRunResult attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryResult attribute) (uchrom.auto_discovery.IterativeDiscoveryResult attribute) (uchrom.auto_discovery.runner.DiscoveryRunResult attribute)

direction_type (uchrom.auto_discovery.DiscoveryDirection attribute) directions_path (uchrom.auto_discovery.DiscoveryRunResult attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryResult attribute) (uchrom.auto_discovery.IterativeDiscoveryResult attribute) (uchrom.auto_discovery.runner.DiscoveryRunResult attribute) directions_to_agent_context() (in module uchrom.auto_discovery) discovery_schema (uchrom.core.ChromData property) DiscoveryBackend (class in uchrom.auto_discovery.backends) DiscoveryDirection (class in uchrom.auto_discovery) DiscoveryEnrichmentConfig (class in uchrom.auto_discovery) DiscoveryFrontier (in module uchrom.auto_discovery) DiscoveryIdea (class in uchrom.auto_discovery) (class in uchrom.auto_discovery.ideas) DiscoveryRunConfig (class in uchrom.auto_discovery) (class in uchrom.auto_discovery.runner) DiscoveryRunResult (class in uchrom.auto_discovery) (class in uchrom.auto_discovery.runner) display_name (uchrom.auto_discovery.backends.CLISpec attribute) (uchrom.auto_discovery.backends.DiscoveryBackend attribute) (uchrom.auto_discovery.backends.PantheonBackend attribute) (uchrom.auto_discovery.CLISpec attribute) distance (uchrom.strc.tad.arc_pval.TADCallerParams attribute) (uchrom.strc.tad.TADCallerParams attribute) downsample_coords() (in module uchrom.recon.bulk.mds.transforms)

E

edges (uchrom.auto_discovery.graph.IdeaGraph attribute) (uchrom.auto_discovery.IdeaGraph attribute) effect_size (uchrom.auto_discovery.EvidenceConclusion attribute) enabled() (uchrom.auto_discovery.DiscoveryEnrichmentConfig method) endpoint_k (uchrom.recon.fish._assembly.AssemblyParams attribute) enrich_for_discovery() (in module uchrom.auto_discovery) enriched_h5cd_path (uchrom.auto_discovery.DiscoveryRunResult attribute) (uchrom.auto_discovery.runner.DiscoveryRunResult attribute) enrichment (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) enrichment_summary_path (uchrom.auto_discovery.DiscoveryRunResult attribute) (uchrom.auto_discovery.runner.DiscoveryRunResult attribute) error (uchrom.auto_discovery.BackendDetection attribute) (uchrom.auto_discovery.backends.BackendDetection attribute) (uchrom.auto_discovery.pantheon.PantheonSchematicRecord attribute) errors (uchrom.auto_discovery.IdeaReview attribute) (uchrom.auto_discovery.ideas.IdeaReview attribute) evidence_basis (uchrom.auto_discovery.DiscoveryDirection attribute) EvidenceConclusion (class in uchrom.auto_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.auto_discovery.backends.CLISpec attribute) (uchrom.auto_discovery.CLISpec attribute) executable_path (uchrom.auto_discovery.BackendDetection attribute) (uchrom.auto_discovery.backends.BackendDetection attribute) execute (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) execute_notebook_python() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.notebooks) expected_direction (uchrom.auto_discovery.DiscoveryIdea attribute) (uchrom.auto_discovery.ideas.DiscoveryIdea attribute) expected_distance() (in module uchrom.im.trace._polymer) expected_distance_sq() (in module uchrom.im.trace._polymer) extra_cells (uchrom.auto_discovery.AnalysisCodeResult attribute) (uchrom.auto_discovery.backends.AnalysisCodeResult attribute) extract_structured_json() (in module uchrom.auto_discovery.backends)

F

fallback_bins (uchrom.auto_discovery.backends.CLISpec attribute) (uchrom.auto_discovery.CLISpec attribute) fasta (uchrom.auto_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_sha256() (in module uchrom.fea.registry) file_workspace (uchrom.auto_discovery.BackendCapabilities attribute) (uchrom.auto_discovery.backends.BackendCapabilities 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) 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_dataframe() (uchrom.core.ChromData class method) from_dict() (uchrom.auto_discovery.DiscoveryIdea class method) (uchrom.auto_discovery.ideas.DiscoveryIdea class method) from_fofct() (uchrom.core.ChromData 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.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) frontier_id (uchrom.auto_discovery.DiscoveryDirection property) frontier_summary_path (uchrom.auto_discovery.DiscoveryRunResult property) (uchrom.auto_discovery.iterative.IterativeDiscoveryResult property) (uchrom.auto_discovery.IterativeDiscoveryResult property) (uchrom.auto_discovery.runner.DiscoveryRunResult property) frontier_type (uchrom.auto_discovery.DiscoveryDirection property) frontiers_path (uchrom.auto_discovery.DiscoveryRunResult property) (uchrom.auto_discovery.iterative.IterativeDiscoveryResult property) (uchrom.auto_discovery.IterativeDiscoveryResult property) (uchrom.auto_discovery.runner.DiscoveryRunResult property) frontiers_to_agent_context() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.frontier)

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.auto_discovery.backends.CLIBackend method) (uchrom.auto_discovery.backends.DiscoveryBackend method) (uchrom.auto_discovery.backends.PantheonBackend method) generate_ideas() (uchrom.auto_discovery.backends.CLIBackend method) (uchrom.auto_discovery.backends.DiscoveryBackend method) (uchrom.auto_discovery.backends.PantheonBackend method) generate_pantheon_ideas() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.pantheon) generate_pantheon_schematic_images_for_run() (in module uchrom.auto_discovery.pantheon) generate_schematic_image (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) get() (uchrom.auto_discovery.DiscoveryIdea method) (uchrom.auto_discovery.ideas.DiscoveryIdea method) get_all_canvas() (uchrom.browser.main_window.MainWindow method) get_backend() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.backends) get_canvas_ix() (uchrom.browser.main_window.MainWindow method) get_cell() (uchrom.core.ChromData method)

get_chrom() (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_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.ChromData method) graph_html_path (uchrom.auto_discovery.DiscoveryRunResult attribute) (uchrom.auto_discovery.runner.DiscoveryRunResult attribute) graph_id (uchrom.auto_discovery.graph.IdeaGraph attribute) (uchrom.auto_discovery.IdeaGraph attribute) graph_path (uchrom.auto_discovery.DiscoveryRunResult attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryResult attribute) (uchrom.auto_discovery.IterativeDiscoveryResult attribute) (uchrom.auto_discovery.runner.DiscoveryRunResult attribute) graph_summary_markdown() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.graph) graph_summary_path (uchrom.auto_discovery.DiscoveryRunResult attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryResult attribute) (uchrom.auto_discovery.IterativeDiscoveryResult attribute) (uchrom.auto_discovery.runner.DiscoveryRunResult attribute) gtf (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute)

H

h5cd_path (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) hash_sources (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) 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.auto_discovery.iterative.IterativeDiscoveryResult attribute) (uchrom.auto_discovery.IterativeDiscoveryResult attribute) hypothesis_status (uchrom.auto_discovery.EvidenceConclusion attribute)

I

idea_agent_count (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) idea_id (uchrom.auto_discovery.DiscoveryIdea attribute) (uchrom.auto_discovery.ideas.DiscoveryIdea attribute) (uchrom.auto_discovery.pantheon.PantheonSchematicRecord attribute) idea_markdown (uchrom.auto_discovery.DiscoveryIdea attribute) (uchrom.auto_discovery.ideas.DiscoveryIdea attribute) idea_output_schema() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.llm) idea_signature() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.graph) idea_source (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) idea_title (uchrom.auto_discovery.DiscoveryIdea attribute) (uchrom.auto_discovery.ideas.DiscoveryIdea attribute) idea_to_markdown() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.notebooks) IdeaGraph (class in uchrom.auto_discovery) (class in uchrom.auto_discovery.graph) IdeaReview (class in uchrom.auto_discovery) (class in uchrom.auto_discovery.ideas) ideas_path (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.DiscoveryRunResult attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunResult attribute)

ideas_per_iteration (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) image_path (uchrom.auto_discovery.pantheon.PantheonSchematicRecord attribute) impute (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) infer_parameter_family() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.graph) ingest_literature_claims() (in module uchrom.auto_discovery) (in module uchrom.auto_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) inter_mds() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.bulk.mds.inter) iteration_results (uchrom.auto_discovery.iterative.IterativeDiscoveryResult attribute) (uchrom.auto_discovery.IterativeDiscoveryResult attribute) iterations (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) iterative (uchrom.recon.fish._assembly.AssemblyParams attribute) IterativeDiscoveryConfig (class in uchrom.auto_discovery) (class in uchrom.auto_discovery.iterative) IterativeDiscoveryResult (class in uchrom.auto_discovery) (class in uchrom.auto_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)

knowledge_mode (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_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) linked_adata (uchrom.core.ChromData property) list_backends() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.backends) llm_timeout (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute)

load_contact_matrix() (in module uchrom.recon.fish._hic) load_cool() (in module uchrom.io) load_idea_graph() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.graph) load_linked_anndata() (uchrom.core.ChromData method) load_model() (uchrom.browser.main_window.MainWindow method) load_session_dialog() (uchrom.browser.main_window.MainWindow method) load_session_file() (uchrom.browser.main_window.MainWindow method) load_tad_from_bed() (in module uchrom.strc.tad) (in module uchrom.strc.tad.utils) 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) MainWindow (class in uchrom.browser.main_window) match_scales (uchrom.recon.fish._assembly.AssemblyParams attribute) max_bins_per_tad (uchrom.recon.fish._intra_tad.Stage2Params attribute) max_complexity (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) max_fibers_per_chrom (uchrom.im.trace.SpotAlignerParams attribute), [1] max_generation_attempts (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) max_ideas (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_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_tol (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) metadata (uchrom.auto_discovery.DiscoveryIdea attribute) (uchrom.auto_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_spots_per_fiber (uchrom.im.trace.SpotAlignerParams attribute), [1] missing_fields (uchrom.auto_discovery.IdeaReview attribute) (uchrom.auto_discovery.ideas.IdeaReview attribute) modalities (uchrom.auto_discovery.DiscoveryIdea attribute) (uchrom.auto_discovery.ideas.DiscoveryIdea attribute) mode (uchrom.auto_discovery.ClaimRefreshResult attribute) model (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.pantheon.PantheonSchematicRecord attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) module uchrom.auto_discovery uchrom.auto_discovery.backends uchrom.auto_discovery.frontier uchrom.auto_discovery.graph uchrom.auto_discovery.ideas uchrom.auto_discovery.iterative uchrom.auto_discovery.llm uchrom.auto_discovery.notebooks uchrom.auto_discovery.pantheon uchrom.auto_discovery.runner uchrom.auto_discovery.schema uchrom.auto_discovery.visualization uchrom.browser uchrom.core 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.pl uchrom.pl.structure_3d uchrom.pl.trace_stats 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.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.utils uchrom.utils.stats

N

n_accepted (uchrom.auto_discovery.DiscoveryRunResult attribute) (uchrom.auto_discovery.runner.DiscoveryRunResult attribute) n_cells (uchrom.core.ChromData property) n_claims (uchrom.auto_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.auto_discovery.DiscoveryRunResult attribute) (uchrom.auto_discovery.runner.DiscoveryRunResult attribute) n_generated (uchrom.auto_discovery.DiscoveryRunResult attribute) (uchrom.auto_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_spots (uchrom.core.ChromData property) n_traces (uchrom.core.ChromData property)

n_verified (uchrom.auto_discovery.DiscoveryRunResult attribute) (uchrom.auto_discovery.runner.DiscoveryRunResult attribute) native_skill_loading (uchrom.auto_discovery.BackendCapabilities attribute) (uchrom.auto_discovery.backends.BackendCapabilities attribute) nodes (uchrom.auto_discovery.graph.IdeaGraph attribute) (uchrom.auto_discovery.IdeaGraph attribute) normalize_distances() (in module uchrom.recon.bulk.mds) notebook (uchrom.auto_discovery.pantheon.PantheonSchematicRecord attribute) notebook_agent_concurrency (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) notebook_status (uchrom.auto_discovery.EvidenceConclusion attribute) notebooks (uchrom.auto_discovery.DiscoveryRunResult attribute) (uchrom.auto_discovery.runner.DiscoveryRunResult attribute) notes (uchrom.auto_discovery.AnalysisCodeResult attribute) (uchrom.auto_discovery.backends.AnalysisCodeResult attribute) (uchrom.auto_discovery.ClaimRefreshResult attribute) novelty_notes (uchrom.auto_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) 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.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.DiscoveryRunResult attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryResult attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryResult attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunResult attribute)

overwrite (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) owns_notebook_lifecycle (uchrom.auto_discovery.BackendCapabilities attribute) (uchrom.auto_discovery.backends.BackendCapabilities attribute)

P

p_value (uchrom.auto_discovery.EvidenceConclusion attribute) pack_schema() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.schema) PantheonAgentRecord (class in uchrom.auto_discovery.pantheon) PantheonBackend (class in uchrom.auto_discovery.backends) PantheonSchematicRecord (class in uchrom.auto_discovery.pantheon) parent_idea_ids (uchrom.auto_discovery.DiscoveryDirection attribute) partitioned_mds() (in module uchrom.recon.bulk.mds) peak_agg (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) peak_control_scale (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) peak_control_tracks (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) peak_cutoff (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) peak_fragment_size_bins (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) peak_genome_size (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) peak_large_local_window_bins (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) peak_max_gap (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) peak_max_gap_bins (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) peak_method (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) peak_min_length (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) peak_min_width_bins (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) peak_negative (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) peak_nolambda (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) peak_pvalue (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) peak_quantile (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) peak_qvalue (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) peak_signal_scale (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) peak_small_local_window_bins (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) peak_threshold (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) peak_tracks (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) persistence_length_bp (uchrom.im.trace.SpotAlignerParams attribute), [1] PERSISTENCE_LENGTH_BP_DEFAULT (in module uchrom.im.trace._polymer) plan_discovery_directions() (in module uchrom.auto_discovery) plan_discovery_frontiers() (in module uchrom.auto_discovery) (in module uchrom.auto_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) prior_graph_path (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) priority (uchrom.auto_discovery.DiscoveryDirection attribute) procrustes_alignment() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.bulk.mds.transforms) project (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) project_existing_structure (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) 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.auto_discovery.DiscoveryEnrichmentConfig attribute) prompt (uchrom.auto_discovery.DiscoveryDirection attribute) prompt_path (uchrom.auto_discovery.BackendAgentRecord attribute) (uchrom.auto_discovery.backends.BackendAgentRecord attribute) (uchrom.auto_discovery.pantheon.PantheonAgentRecord attribute) (uchrom.auto_discovery.pantheon.PantheonSchematicRecord attribute) prompt_via_stdin (uchrom.auto_discovery.BackendCapabilities attribute) (uchrom.auto_discovery.backends.BackendCapabilities attribute) 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.auto_discovery.DiscoveryDirection attribute) read() (uchrom.core.ChromData class method) read_bedgraph() (in module uchrom.fea) (in module uchrom.fea.peaks) read_gtf() (in module uchrom.fea) (in module uchrom.fea.annotation) read_pairs() (in module uchrom.io) read_particles() (in module uchrom.io) reasoning_effort (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) reconstruct_gem_fish() (in module uchrom.recon.fish), [1] reconstruct_intra_tad() (in module uchrom.recon.fish._intra_tad) reconstruct_tad_level() (in module uchrom.recon.fish._tad_level) reflect_threshold (uchrom.recon.fish._assembly.AssemblyParams attribute) refresh_literature_claims_for_iteration() (in module uchrom.auto_discovery) register_backend() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.backends) remove_canvas() (uchrom.browser.main_window.MainWindow method) remove_violated_contacts() (in module uchrom.io) report_path (uchrom.auto_discovery.DiscoveryRunResult attribute) (uchrom.auto_discovery.runner.DiscoveryRunResult attribute) required_fields (uchrom.auto_discovery.DiscoveryIdea attribute) (uchrom.auto_discovery.ideas.DiscoveryIdea attribute)

resizeEvent() (uchrom.browser.main_window.MainWindow method) resolution (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) results_path (uchrom.auto_discovery.DiscoveryRunResult attribute) (uchrom.auto_discovery.runner.DiscoveryRunResult attribute) resume (uchrom.auto_discovery.BackendCapabilities attribute) (uchrom.auto_discovery.backends.BackendCapabilities attribute) retrieval_log_path (uchrom.auto_discovery.ClaimRefreshResult attribute) review_idea_against_schema() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.ideas) reviews_path (uchrom.auto_discovery.DiscoveryRunResult attribute) (uchrom.auto_discovery.runner.DiscoveryRunResult attribute) rg_loss() (in module uchrom.recon.fish._losses) rg_squared() (in module uchrom.recon.fish._losses) role (uchrom.auto_discovery.BackendAgentRecord attribute) (uchrom.auto_discovery.backends.BackendAgentRecord attribute) (uchrom.auto_discovery.pantheon.PantheonAgentRecord attribute) run_auto_discovery() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.runner) run_dirs (uchrom.auto_discovery.iterative.IterativeDiscoveryResult attribute) (uchrom.auto_discovery.IterativeDiscoveryResult attribute) run_environment() (uchrom.auto_discovery.backends.CLISpec method) (uchrom.auto_discovery.CLISpec method) run_iterative_auto_discovery() (in module uchrom.auto_discovery) (in module uchrom.auto_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.auto_discovery) (in module uchrom.auto_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.auto_discovery) (in module uchrom.auto_discovery.schema) schematic_coverage_for_run() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.pantheon) schematic_image_model (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) schematic_image_model_args (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) seed_run_dirs (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) sequence_features (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) sister_pair_radius_nm (uchrom.im.trace.SpotAlignerParams attribute), [1] 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) source_paths (uchrom.auto_discovery.ClaimRefreshResult attribute) SpotAlignerParams (class in uchrom.im.trace), [1] stable_idea_id() (in module uchrom.auto_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.auto_discovery.pantheon.PantheonSchematicRecord attribute) stop_on_error (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) store_schema (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.iterative.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.IterativeDiscoveryConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) stream_format (uchrom.auto_discovery.backends.CLISpec attribute) (uchrom.auto_discovery.CLISpec attribute) streaming (uchrom.auto_discovery.BackendCapabilities attribute) (uchrom.auto_discovery.backends.BackendCapabilities attribute) structured_conclusion_markdown() (in module uchrom.auto_discovery) structured_output (uchrom.auto_discovery.BackendCapabilities attribute) (uchrom.auto_discovery.backends.BackendCapabilities attribute) structures (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) substructures_from_tads() (in module uchrom.strc.tad) (in module uchrom.strc.tad.utils) summary (uchrom.auto_discovery.EvidenceConclusion attribute) summary() (uchrom.auto_discovery.graph.IdeaGraph method) (uchrom.auto_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) target_facets (uchrom.auto_discovery.DiscoveryDirection attribute) tau_nm_per_bp (uchrom.im.trace.SpotAlignerParams attribute), [1] 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.auto_discovery.DiscoveryDirection attribute) to_anndata() (uchrom.core.ChromData method) to_dataframe() (uchrom.core.ChromData method) to_dict() (uchrom.auto_discovery.ClaimRefreshResult method) (uchrom.auto_discovery.DiscoveryDirection method) (uchrom.auto_discovery.DiscoveryIdea method) (uchrom.auto_discovery.graph.IdeaGraph method) (uchrom.auto_discovery.IdeaGraph method) (uchrom.auto_discovery.IdeaReview method) (uchrom.auto_discovery.ideas.DiscoveryIdea method) (uchrom.auto_discovery.ideas.IdeaReview method) (uchrom.auto_discovery.iterative.IterativeDiscoveryResult method) (uchrom.auto_discovery.IterativeDiscoveryResult method) torch_mds() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.bulk.mds.torch_mds) trigger_other_canvas_mouse_event() (uchrom.browser.main_window.MainWindow method)

U

uchrom.auto_discovery module uchrom.auto_discovery.backends module uchrom.auto_discovery.frontier module uchrom.auto_discovery.graph module uchrom.auto_discovery.ideas module uchrom.auto_discovery.iterative module uchrom.auto_discovery.llm module uchrom.auto_discovery.notebooks module uchrom.auto_discovery.pantheon module uchrom.auto_discovery.runner module uchrom.auto_discovery.schema module uchrom.auto_discovery.visualization module uchrom.browser module uchrom.core 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.pl module

uchrom.pl.structure_3d module uchrom.pl.trace_stats 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.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.utils module uchrom.utils.stats module unique_spot_intervals() (in module uchrom.fea) (in module uchrom.fea.project) unpack_schema() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.schema) unregister_backend() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.backends) update_canvas_border_color() (uchrom.browser.main_window.MainWindow method) update_discovery_schema() (uchrom.core.ChromData method) upsert_structured_conclusion() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.notebooks) user_annotations (uchrom.core.ChromData property)

V

validate_discovery_schema() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.schema) (uchrom.core.ChromData method) validation_checks (uchrom.auto_discovery.DiscoveryIdea attribute) (uchrom.auto_discovery.ideas.DiscoveryIdea attribute) verbose (uchrom.auto_discovery.DiscoveryEnrichmentConfig attribute) (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]

version (uchrom.auto_discovery.BackendDetection attribute) (uchrom.auto_discovery.backends.BackendDetection attribute) visual_qa (uchrom.auto_discovery.pantheon.PantheonSchematicRecord attribute)

W

warnings (uchrom.auto_discovery.AnalysisCodeResult attribute) (uchrom.auto_discovery.backends.AnalysisCodeResult attribute) (uchrom.auto_discovery.IdeaReview attribute) (uchrom.auto_discovery.ideas.IdeaReview 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.ChromData method) write_direction_artifacts() (in module uchrom.auto_discovery)

write_frontier_artifacts() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.frontier) write_idea_graph_artifacts() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.graph) write_idea_graph_html() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.visualization) write_json() (uchrom.auto_discovery.graph.IdeaGraph method) (uchrom.auto_discovery.IdeaGraph method) write_summary_markdown() (uchrom.auto_discovery.graph.IdeaGraph method) (uchrom.auto_discovery.IdeaGraph method)