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) 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_widgets() (uchrom.browser.main_window.MainWindow method) adjust_camera() (uchrom.browser.main_window.MainWindow method) agent_name (uchrom.auto_discovery.pantheon.PantheonAgentRecord attribute) agent_records_path (uchrom.auto_discovery.DiscoveryRunResult attribute) (uchrom.auto_discovery.runner.DiscoveryRunResult attribute) aggregate_over_tads() (in module uchrom.recon.fish._hic) 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) alpha (uchrom.recon.fish._assembly.AssemblyParams attribute) analysis_plan (uchrom.auto_discovery.DiscoveryIdea attribute) (uchrom.auto_discovery.ideas.DiscoveryIdea attribute) angle_weight (uchrom.recon.fish._intra_tad.Stage2Params attribute) (uchrom.recon.fish._tad_level.Stage1Params attribute) 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) assemble() (in module uchrom.recon.fish._assembly) AssemblyParams (class in uchrom.recon.fish._assembly) auto_discovery_schema (uchrom.core.ChromData property) axis_variance_cube() (in module uchrom.fea) (in module uchrom.fea.arc) axis_weight() (in module uchrom.fea) (in module uchrom.fea.arc)

B

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_discovery_schema() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.schema) (uchrom.core.ChromData method)

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_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_tads_by_pval() (in module uchrom.strc.tad) (in module uchrom.strc.tad.arc_pval) 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.core.ChromData property) classify_hypothesis_evidence() (in module uchrom.auto_discovery) cmds_init() (in module uchrom.recon.bulk.mds.torch_mds) code_source (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) 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_distances() (uchrom.core.ChromData method) compute_radius_of_gyration() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.bulk.mds.transforms) compute_stress() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.bulk.mds.torch_mds) 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.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.runner.DiscoveryRunConfig attribute) 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_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]

direction_status (uchrom.auto_discovery.EvidenceConclusion attribute) discovery_schema (uchrom.core.ChromData property) 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) distance (uchrom.strc.tad.arc_pval.TADCallerParams attribute) (uchrom.strc.tad.TADCallerParams attribute) downsample_coords() (in module uchrom.recon.bulk.mds.transforms)

E

effect_size (uchrom.auto_discovery.EvidenceConclusion attribute) endpoint_k (uchrom.recon.fish._assembly.AssemblyParams attribute) error (uchrom.auto_discovery.pantheon.PantheonSchematicRecord attribute) errors (uchrom.auto_discovery.IdeaReview attribute) (uchrom.auto_discovery.ideas.IdeaReview 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)

execute (uchrom.auto_discovery.DiscoveryRunConfig 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)

F

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) 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)

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_openai_analysis_code() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.llm) generate_openai_ideas() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.llm) 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.runner.DiscoveryRunConfig attribute)

get_all_canvas() (uchrom.browser.main_window.MainWindow method) 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)

H

h5cd_path (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig 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) hypothesis_status (uchrom.auto_discovery.EvidenceConclusion attribute)

I

idea_agent_count (uchrom.auto_discovery.DiscoveryRunConfig 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_source (uchrom.auto_discovery.DiscoveryRunConfig 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) 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)

image_path (uchrom.auto_discovery.pantheon.PantheonSchematicRecord attribute) impute (uchrom.strc.tad.fishnet.FISHnetParams attribute) (uchrom.strc.tad.FISHnetParams attribute) 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) iterative (uchrom.recon.fish._assembly.AssemblyParams attribute)

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)

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) llm_timeout (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute)

load_contact_matrix() (in module uchrom.recon.fish._hic) load_cool() (in module uchrom.io) 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

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.runner.DiscoveryRunConfig attribute) max_fibers_per_chrom (uchrom.im.trace.SpotAlignerParams attribute), [1] 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) model (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.pantheon.PantheonSchematicRecord attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) module uchrom.auto_discovery uchrom.auto_discovery.ideas uchrom.auto_discovery.llm uchrom.auto_discovery.notebooks uchrom.auto_discovery.pantheon uchrom.auto_discovery.runner uchrom.auto_discovery.schema uchrom.browser uchrom.core uchrom.fea uchrom.fea.arc uchrom.fea.distance 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.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_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) 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.runner.DiscoveryRunConfig attribute) notebook_status (uchrom.auto_discovery.EvidenceConclusion attribute) notebooks (uchrom.auto_discovery.DiscoveryRunResult attribute) (uchrom.auto_discovery.runner.DiscoveryRunResult 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.runner.DiscoveryRunConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunResult 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) PantheonSchematicRecord (class in uchrom.auto_discovery.pantheon) partitioned_mds() (in module uchrom.recon.bulk.mds) persistence_length_bp (uchrom.im.trace.SpotAlignerParams attribute), [1] PERSISTENCE_LENGTH_BP_DEFAULT (in module uchrom.im.trace._polymer) 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) procrustes_alignment() (in module uchrom.recon.bulk.mds) (in module uchrom.recon.bulk.mds.transforms) prominence (uchrom.strc.tad.arc_pval.TADCallerParams attribute) (uchrom.strc.tad.TADCallerParams attribute) prompt_path (uchrom.auto_discovery.pantheon.PantheonAgentRecord attribute) (uchrom.auto_discovery.pantheon.PantheonSchematicRecord 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) read() (uchrom.core.ChromData class method) read_pairs() (in module uchrom.io) read_particles() (in module uchrom.io) reasoning_effort (uchrom.auto_discovery.DiscoveryRunConfig 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) 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) 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.pantheon.PantheonAgentRecord attribute) run_auto_discovery() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.runner) 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_image_model (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig attribute) schematic_image_model_args (uchrom.auto_discovery.DiscoveryRunConfig attribute) (uchrom.auto_discovery.runner.DiscoveryRunConfig 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) 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.runner.DiscoveryRunConfig attribute) structured_conclusion_markdown() (in module uchrom.auto_discovery) substructures_from_tads() (in module uchrom.strc.tad) (in module uchrom.strc.tad.utils) summary (uchrom.auto_discovery.EvidenceConclusion attribute)

T

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) 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) to_anndata() (uchrom.core.ChromData method) to_dataframe() (uchrom.core.ChromData method) to_dict() (uchrom.auto_discovery.DiscoveryIdea method) (uchrom.auto_discovery.IdeaReview method) (uchrom.auto_discovery.ideas.DiscoveryIdea method) (uchrom.auto_discovery.ideas.IdeaReview 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.ideas 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.browser module uchrom.core module uchrom.fea module uchrom.fea.arc module uchrom.fea.distance 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.loop module uchrom.strc.tad module uchrom.strc.tad.di module uchrom.strc.tad.utils module uchrom.utils module uchrom.utils.stats module unpack_schema() (in module uchrom.auto_discovery) (in module uchrom.auto_discovery.schema) 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)

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.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] visual_qa (uchrom.auto_discovery.pantheon.PantheonSchematicRecord attribute)

W

warnings (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)