Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X _ __getattr__() (in module phaselab.quantum) __init__() (phaselab.crispr.CrisporValidator method) __post_init__() (phaselab.quantum.QuantumConfig method) A A (phaselab.crispr.GuideTier attribute) (phaselab.integrations.crispor.EvidenceLevel attribute) abc_score (phaselab.crispr.Enhancer attribute) abs_end (phaselab.crispr.EnhancedGuide attribute) abs_start (phaselab.crispr.EnhancedGuide attribute) absolute_E (phaselab.crispr.BindingEnergyResult attribute) accessibility (phaselab.crispr.EnhancedGuide attribute) activation_potential (phaselab.crispr.EnhancerGuideResult attribute) activity_score (phaselab.crispr.Enhancer attribute) activity_window (phaselab.crispr.BaseEditConfig attribute) add_region() (phaselab.crispr.RegionSet method) add_tss() (phaselab.crispr.RegionBuilder method) add_tss_manual() (phaselab.crispr.RegionBuilder method) add_window() (phaselab.crispr.RegionBuilder method) alpha_P (phaselab.circadian.SMSClockParams attribute) amplitudes (phaselab.circadian.MultiTissueResult attribute) analyze_guide_pair() (in module phaselab.crispr) analyze_offtarget_landscape() (in module phaselab.integrations.crispor) apply_hard_gates() (in module phaselab.crispr) ASCAS12A (phaselab.crispr.Nuclease attribute) ATLAS_Q_EXPECTATIONS (phaselab.integrations.crispor.CoherenceSource attribute) ATLAS_Q_VQE (phaselab.integrations.crispor.CoherenceSource attribute) AUDIT (phaselab.quantum.QuantumMode attribute) audit_fraction (phaselab.quantum.QuantumConfig attribute) B B (phaselab.crispr.GuideTier attribute) (phaselab.integrations.crispor.EvidenceLevel attribute) backend (phaselab.quantum.QuantumConfig attribute) BASE_EDITING (phaselab.crispr.Modality attribute) BaseEditConfig (class in phaselab.crispr) benchmark_against_published() (in module phaselab.crispr) BenchmarkResult (class in phaselab.crispr) beta_R (phaselab.circadian.SMSClockParams attribute) beta_V (phaselab.circadian.SMSClockParams attribute) BINDING (phaselab.crispr.NucleaseRole attribute) binding_energy (phaselab.crispr.QuantumGuideResult attribute) (phaselab.integrations.crispor.OffTargetSite attribute) binding_result (phaselab.crispr.MultiEvidenceResult attribute) BINDING_STRICT (phaselab.crispr.RankingPolicy attribute) BindingEnergyResult (class in phaselab.crispr) bonus_diffuse_risk (phaselab.integrations.crispor.ScoringWeights attribute) build() (phaselab.crispr.RegionBuilder method) build_regions_for_gene() (in module phaselab.crispr) C C (phaselab.crispr.GuideTier attribute) (phaselab.integrations.crispor.EvidenceLevel attribute) CandidateGuide (class in phaselab.crispr) candidates (phaselab.crispr.EnumerationResult attribute) candidates_by_region (phaselab.crispr.EnumerationResult property) candidates_by_strand (phaselab.crispr.EnumerationResult property) CAS9_HF1 (phaselab.crispr.Nuclease attribute) cell_type (phaselab.crispr.EnhancedGuideConfig attribute) center (phaselab.crispr.Enhancer property) cfd_score (phaselab.crispr.CRISPORMetrics attribute) (phaselab.crispr.EnhancedGuide attribute) (phaselab.integrations.crispor.CrisporOffTarget attribute) (phaselab.integrations.crispor.OffTargetSite attribute) cfd_score() (in module phaselab.crispr) cfd_specificity (phaselab.integrations.crispor.CrisporGuideRow attribute) (phaselab.integrations.crispor.GuideCandidate attribute) check_bystanders (phaselab.crispr.BaseEditConfig attribute) check_safety_gate() (in module phaselab.integrations.crispor) check_secondary_structure (phaselab.crispr.PrimeEditConfig attribute) chrom (phaselab.crispr.EnhancedGuide attribute) (phaselab.crispr.Enhancer attribute) (phaselab.integrations.crispor.CrisporGuideRow attribute) (phaselab.integrations.crispor.CrisporOffTarget attribute) chromatin_accessibility_score() (in module phaselab.crispr) chromatin_state (phaselab.crispr.EnhancedGuide attribute) chromosome (phaselab.crispr.CandidateGuide attribute) (phaselab.crispr.Region attribute) (phaselab.crispr.TSSAnnotation attribute) claim_description (phaselab.crispr.EnhancedGuide attribute) claim_level (phaselab.crispr.EnhancedGuide attribute) claim_level_enum (phaselab.crispr.EnhancedGuide property) clash_radius (phaselab.crispr.MultiGuideConfig attribute) classical_scores (phaselab.crispr.DiscriminatorResult attribute) classification (phaselab.circadian.MultiTissueResult attribute) classify_coherence() (in module phaselab.core.coherence) classify_synchronization() (in module phaselab.circadian) close_offtargets (phaselab.integrations.crispor.OffTargetIRAnalysis attribute) cluster_concentration (phaselab.integrations.crispor.OffTargetIRAnalysis attribute) coherence (phaselab.crispr.BindingEnergyResult attribute) (phaselab.crispr.EnhancedGuide attribute) (phaselab.crispr.QuantumGuideResult attribute) coherence_mode (phaselab.crispr.EnhancedGuide attribute) (phaselab.crispr.EnhancedGuideConfig attribute) coherence_R (phaselab.crispr.EnhancerGuideResult attribute) (phaselab.crispr.GuideCandidate attribute) coherence_score() (in module phaselab.core.coherence) coherence_shots (phaselab.crispr.BaseEditConfig attribute) (phaselab.crispr.CRISPRiConfig attribute) (phaselab.crispr.GuideDesignConfig attribute) (phaselab.crispr.KnockoutConfig attribute) (phaselab.crispr.PrimeEditConfig attribute) coherence_source (phaselab.integrations.crispor.GuideCandidate attribute) CoherenceMode (class in phaselab.crispr) (class in phaselab.crispr.coherence_utils) CoherenceResult (class in phaselab.quantum.coherence) CoherenceSource (class in phaselab.integrations.crispor) combined_efficiency (phaselab.crispr.GuidePair attribute) combined_score (phaselab.crispr.EnhancerGuideResult attribute) (phaselab.crispr.MultiEvidenceResult attribute) (phaselab.crispr.MultiGuideSet attribute) compare_coherence() (in module phaselab.quantum.coherence) compare_guides_with_without_context() (in module phaselab.crispr) compare_promoter_vs_enhancer() (in module phaselab.crispr) compare_sim_hardware() (in module phaselab.core.coherence) complexity (phaselab.crispr.EnhancedGuide attribute) compute_binding_energy() (in module phaselab.crispr) compute_binding_landscape() (in module phaselab.crispr) compute_coherence (phaselab.crispr.BaseEditConfig attribute) (phaselab.crispr.CRISPRiConfig attribute) (phaselab.crispr.GuideDesignConfig attribute) (phaselab.crispr.KnockoutConfig attribute) (phaselab.crispr.MultiGuideConfig attribute) (phaselab.crispr.PrimeEditConfig attribute) compute_coherence_batch() (in module phaselab.crispr) (in module phaselab.crispr.coherence_utils) compute_coherence_contrast() (in module phaselab.integrations.crispor) compute_coherence_from_expectations() (in module phaselab.quantum.coherence) compute_coherence_from_hamiltonian() (in module phaselab.quantum.coherence) compute_coherence_from_phases() (in module phaselab.quantum.coherence) compute_coherence_with_zscore() (in module phaselab.crispr) (in module phaselab.crispr.coherence_utils) compute_concentration_measures() (in module phaselab.integrations.crispor) compute_efficiency (phaselab.crispr.CrisporConfig attribute) compute_energy_spectrum() (in module phaselab.integrations.crispor) compute_evidence_level() (phaselab.integrations.crispor.GuideCandidate method) compute_final_score() (in module phaselab.integrations.crispor) compute_geometry_landscape() (in module phaselab.crispr) compute_guide_coherence (phaselab.crispr.GuideDesignConfig attribute) compute_guide_coherence() (in module phaselab.crispr) (in module phaselab.crispr.coherence_utils) compute_guide_coherence_with_details() (in module phaselab.crispr) (in module phaselab.crispr.coherence_utils) compute_ir_enhanced_score() (in module phaselab.integrations.crispor) compute_multi_evidence_score() (in module phaselab.crispr) compute_offtarget_clustering() (in module phaselab.integrations.crispor) compute_offtarget_entropy() (in module phaselab.integrations.crispor) compute_offtarget_geometry() (in module phaselab.crispr) compute_phase_alignment() (in module phaselab.crispr) compute_phase_landscape() (in module phaselab.crispr) compute_region_difficulty() (in module phaselab.integrations.crispor) compute_risk_mass() (in module phaselab.integrations.crispor) compute_tail_risk() (in module phaselab.integrations.crispor) config (phaselab.crispr.EnhancedDesignResult attribute) configure_quantum() (in module phaselab.quantum) context_confidence (phaselab.crispr.EnhancedGuide attribute) crispor_composite_score() (in module phaselab.crispr) crispor_path (phaselab.crispr.CrisporConfig attribute) (phaselab.integrations.crispor.CrisporConfig attribute) crispor_script (phaselab.integrations.crispor.CrisporClient property) crispor_validated (phaselab.integrations.crispor.GuideCandidate attribute) CrisporClient (class in phaselab.integrations.crispor) CrisporConfig (class in phaselab.crispr) (class in phaselab.integrations.crispor) CrisporGuideRow (class in phaselab.integrations.crispor) CRISPORMetrics (class in phaselab.crispr) CrisporOffTarget (class in phaselab.integrations.crispor) CrisporOutput (class in phaselab.integrations.crispor) CrisporValidator (class in phaselab.crispr) crispr_window (phaselab.crispr.GuideDesignConfig attribute) CRISPRA (phaselab.crispr.Modality attribute) crispra_window (phaselab.crispr.EnhancedGuideConfig attribute) CRISPRI (phaselab.crispr.Modality attribute) crispri_window (phaselab.crispr.CRISPRiConfig attribute) (phaselab.crispr.EnhancedGuideConfig attribute) CRISPRiConfig (class in phaselab.crispr) critical_window (phaselab.crispr.PhaseAlignmentResult attribute) CUSTOM (phaselab.crispr.TSSSource attribute) cut_efficiency_score() (in module phaselab.crispr) CUTTING (phaselab.crispr.NucleaseRole attribute) CUTTING_STRICT (phaselab.crispr.RankingPolicy attribute) D delta_E (phaselab.crispr.BindingEnergyResult attribute) delta_g (phaselab.crispr.EnhancedGuide attribute) delta_g_santalucia() (in module phaselab.crispr) delta_R (phaselab.crispr.OffTargetGeometryResult attribute) delta_r_bar (phaselab.integrations.crispor.GuideCandidate attribute) (phaselab.integrations.crispor.OffTargetIRAnalysis attribute) delta_r_bar_threshold (phaselab.integrations.crispor.ScoringWeights attribute) description (phaselab.crispr.PolicyConfig attribute) design_abe_guides() (in module phaselab.crispr) design_base_edit_guides() (in module phaselab.crispr) design_cbe_guides() (in module phaselab.crispr) design_crispra_guides() (in module phaselab.crispr) design_crispra_guides_v2() (in module phaselab.crispr) design_crispri_guides() (in module phaselab.crispr) design_enhanced_guides() (in module phaselab.crispr) design_enhancer_guides() (in module phaselab.crispr) design_guides() (in module phaselab.crispr) design_guides_with_crispor() (in module phaselab.integrations.crispor) design_guides_with_quantum_discriminator() (in module phaselab.crispr) design_knockout_guides() (in module phaselab.crispr) design_knockout_guides_v2() (in module phaselab.crispr) design_multiguide_set() (in module phaselab.crispr) design_pbs() (in module phaselab.crispr) design_prime_edit() (in module phaselab.crispr) design_rt_template() (in module phaselab.crispr) DesignResult (class in phaselab.crispr) details (phaselab.crispr.BenchmarkResult attribute) (phaselab.crispr.BindingEnergyResult attribute) (phaselab.crispr.MultiEvidenceResult attribute) (phaselab.crispr.OffTargetGeometryResult attribute) (phaselab.crispr.PhaseAlignmentResult attribute) (phaselab.crispr.QuantumGuideResult attribute) DiscriminatorResult (class in phaselab.crispr) DiscriminatorStatus (class in phaselab.crispr) disease_severity (phaselab.circadian.MultiTissueParams attribute) disease_tissue (phaselab.circadian.MultiTissueParams attribute) distance_to_tss (phaselab.crispr.Enhancer attribute) doench_2016 (phaselab.integrations.crispor.CrisporGuideRow attribute) (phaselab.integrations.crispor.GuideCandidate attribute) downstream (phaselab.crispr.Window attribute) E ECAS9 (phaselab.crispr.Nuclease attribute) edit_type (phaselab.crispr.PrimeEditConfig attribute) editing_efficiency_at_position() (in module phaselab.crispr) editor (phaselab.crispr.BaseEditConfig attribute) efficiency (phaselab.crispr.GuideCandidate attribute) element_type (phaselab.crispr.Enhancer attribute) emit_manifest() (in module phaselab.crispr) enable_synergy (phaselab.crispr.MultiGuideConfig attribute) end (phaselab.crispr.CandidateGuide attribute) (phaselab.crispr.Enhancer attribute) (phaselab.crispr.Region attribute) (phaselab.integrations.crispor.CrisporGuideRow attribute) (phaselab.integrations.crispor.CrisporOffTarget attribute) energy_off_max (phaselab.integrations.crispor.OffTargetIRAnalysis attribute) energy_off_mean (phaselab.integrations.crispor.OffTargetIRAnalysis attribute) energy_on_target (phaselab.integrations.crispor.OffTargetIRAnalysis attribute) energy_separations (phaselab.crispr.DiscriminatorResult attribute) energy_tail_risk (phaselab.integrations.crispor.OffTargetIRAnalysis attribute) energy_uncertainty (phaselab.crispr.QuantumGuideResult attribute) EnhancedDesignResult (class in phaselab.crispr) EnhancedGuide (class in phaselab.crispr) EnhancedGuideConfig (class in phaselab.crispr) enhancement_factor (phaselab.crispr.PhaseAlignmentResult attribute) Enhancer (class in phaselab.crispr) enhancer (phaselab.crispr.EnhancerGuideResult attribute) EnhancerConfig (class in phaselab.crispr) EnhancerGuideResult (class in phaselab.crispr) ENSEMBL (phaselab.crispr.TSSSource attribute) ensemble_coherence (phaselab.crispr.MultiGuideSet attribute) ensemble_coherence() (in module phaselab.core.coherence) entropy (phaselab.integrations.crispor.OffTargetIRAnalysis attribute) entropy_high_threshold (phaselab.integrations.crispor.ScoringWeights attribute) entropy_low_threshold (phaselab.integrations.crispor.ScoringWeights attribute) entropy_normalized (phaselab.integrations.crispor.OffTargetIRAnalysis attribute) enumerate_from_sequence() (in module phaselab.crispr) enumerate_guides() (in module phaselab.crispr) enumeration (phaselab.crispr.DesignResult attribute) EnumerationResult (class in phaselab.crispr) eqtl_support (phaselab.crispr.Enhancer attribute) error_on_unavailable (phaselab.quantum.QuantumConfig attribute) estimate_hairpin_dg() (in module phaselab.crispr) evaluate_candidate() (in module phaselab.crispr) evaluate_candidates() (in module phaselab.crispr) evidence (phaselab.crispr.BindingEnergyResult attribute) (phaselab.crispr.OffTargetGeometryResult attribute) (phaselab.crispr.PhaseAlignmentResult attribute) evidence_level (phaselab.crispr.EnhancedGuide attribute) (phaselab.integrations.crispor.GuideCandidate attribute) evidence_levels (phaselab.crispr.MultiEvidenceResult attribute) EvidenceLevel (class in phaselab.integrations.crispor) excluded_by (phaselab.crispr.GateResult attribute) execution_time_s (phaselab.crispr.QuantumGuideResult attribute) EXPLORATORY (phaselab.crispr.RankingPolicy attribute) F failed_gates (phaselab.crispr.EnhancedGuide attribute) feeding_amplitude (phaselab.circadian.MultiTissueParams attribute) feeding_phase (phaselab.circadian.MultiTissueParams attribute) filter_poly_t (phaselab.crispr.GuideDesignConfig attribute) filter_repeats (phaselab.crispr.GuideDesignConfig attribute) filtered_by_coherence (phaselab.crispr.EnhancedDesignResult attribute) filtered_by_gates (phaselab.crispr.EnhancedDesignResult attribute) final_score (phaselab.integrations.crispor.GuideCandidate attribute) find_bystanders() (in module phaselab.crispr) find_pam_sites() (in module phaselab.crispr) frameshift_probability() (in module phaselab.crispr) full_sequence (phaselab.integrations.crispor.GuideCandidate property) fused_confidence (phaselab.crispr.EnhancedGuide attribute) fused_score (phaselab.crispr.EnhancedGuide attribute) fusion_config (phaselab.crispr.EnhancedGuideConfig attribute) G gate_0mm (phaselab.crispr.PolicyConfig attribute) gate_1mm (phaselab.crispr.PolicyConfig attribute) gate_repeats (phaselab.crispr.PolicyConfig attribute) gate_u6_incompatible (phaselab.crispr.PolicyConfig attribute) gate_unscorable (phaselab.crispr.PolicyConfig attribute) GateResult (class in phaselab.crispr) gc (phaselab.crispr.EnhancedGuide attribute) gc_content() (in module phaselab.crispr) GENCODE (phaselab.crispr.TSSSource attribute) gene (phaselab.integrations.crispor.CrisporOffTarget attribute) (phaselab.integrations.crispor.OffTargetSite attribute) gene_id (phaselab.crispr.Region attribute) (phaselab.crispr.RegionSet attribute) (phaselab.crispr.TSSAnnotation attribute) gene_region (phaselab.integrations.crispor.CrisporOffTarget attribute) gene_symbol (phaselab.crispr.BenchmarkResult attribute) (phaselab.crispr.DesignResult attribute) (phaselab.crispr.Region attribute) (phaselab.crispr.RegionSet attribute) (phaselab.crispr.TSSAnnotation attribute) generate_report() (in module phaselab.integrations.crispor) genome (phaselab.crispr.CrisporConfig attribute) (phaselab.integrations.crispor.CrisporConfig attribute) genome_build (phaselab.crispr.DesignResult attribute) (phaselab.crispr.Region attribute) (phaselab.crispr.RegionSet attribute) genome_dir (phaselab.integrations.crispor.CrisporConfig attribute) GenomeBuild (class in phaselab.crispr) geometry_result (phaselab.crispr.MultiEvidenceResult attribute) get_activity_window() (in module phaselab.crispr) get_atlas_q_version() (in module phaselab.quantum) get_backend_info() (phaselab.quantum.QuantumConfig method) get_coherence_eligibility_info() (in module phaselab.crispr) (in module phaselab.crispr.coherence_utils) get_coherence_method() (in module phaselab.crispr) (in module phaselab.crispr.coherence_utils) get_known_enhancers() (in module phaselab.crispr) get_pam_display() (phaselab.crispr.NucleaseConfig method) get_pam_pattern() (phaselab.crispr.NucleaseConfig method) get_quantum_config() (in module phaselab.quantum) get_quantum_mode() (in module phaselab.quantum) get_tss_for_gene() (in module phaselab.crispr) gini_coefficient (phaselab.integrations.crispor.GuideCandidate attribute) global_R_bar (phaselab.circadian.MultiTissueResult attribute) go_guides (phaselab.crispr.EnhancedDesignResult property) go_no_go (phaselab.circadian.MultiTissueResult attribute) (phaselab.crispr.EnhancerGuideResult attribute) (phaselab.crispr.MultiGuideSet attribute) go_no_go() (in module phaselab.core.coherence) go_reason (phaselab.crispr.EnhancedGuide attribute) go_status (phaselab.crispr.EnhancedGuide attribute) go_threshold (phaselab.crispr.EnhancedGuideConfig attribute) guide1 (phaselab.crispr.GuidePair attribute) guide2 (phaselab.crispr.GuidePair attribute) guide_id (phaselab.crispr.CandidateGuide property) (phaselab.integrations.crispor.CrisporGuideRow attribute) (phaselab.integrations.crispor.CrisporOffTarget attribute) guide_length (phaselab.crispr.BaseEditConfig attribute) (phaselab.crispr.CRISPRiConfig attribute) (phaselab.crispr.EnhancedGuideConfig attribute) (phaselab.crispr.GuideDesignConfig attribute) (phaselab.crispr.KnockoutConfig attribute) (phaselab.crispr.NucleaseConfig attribute) (phaselab.crispr.PrimeEditConfig attribute) guide_length_range (phaselab.crispr.NucleaseConfig attribute) guide_position (phaselab.crispr.EnhancerGuideResult attribute) guide_quality (phaselab.crispr.EnhancerGuideResult attribute) guide_sequence (phaselab.crispr.EnhancerGuideResult attribute) (phaselab.crispr.QuantumGuideResult attribute) (phaselab.integrations.crispor.OffTargetIRAnalysis attribute) GuideCandidate (class in phaselab.crispr) (class in phaselab.integrations.crispor) GuideDesignConfig (class in phaselab.crispr) GuidePair (class in phaselab.crispr) guides (phaselab.crispr.EnhancedDesignResult attribute) (phaselab.crispr.MultiGuideSet attribute) guides_per_enhancer (phaselab.crispr.EnhancerConfig attribute) guides_tsv (phaselab.integrations.crispor.CrisporOutput attribute) GuideTier (class in phaselab.crispr) H HARDWARE (phaselab.integrations.crispor.CoherenceSource attribute) hardware_backend (phaselab.crispr.GuideDesignConfig attribute) has_clashes (phaselab.crispr.MultiGuideSet attribute) has_critical_disagreement (phaselab.crispr.EnhancedGuide attribute) has_exonic_close_offtargets (phaselab.integrations.crispor.CrisporGuideRow property) has_exonic_close_ot (phaselab.integrations.crispor.GuideCandidate attribute) (phaselab.integrations.crispor.OffTargetIRAnalysis attribute) has_exonic_risk (phaselab.integrations.crispor.OffTargetIRAnalysis attribute) has_experimental_data (phaselab.integrations.crispor.GuideCandidate attribute) has_steric_clash (phaselab.crispr.GuidePair attribute) herfindahl_index (phaselab.integrations.crispor.GuideCandidate attribute) HEURISTIC (phaselab.crispr.coherence_utils.CoherenceMode attribute) (phaselab.crispr.CoherenceMode attribute) (phaselab.integrations.crispor.CoherenceSource attribute) HG19 (phaselab.crispr.GenomeBuild attribute) HG38 (phaselab.crispr.GenomeBuild attribute) hi_c_contact (phaselab.crispr.Enhancer attribute) histone_activity (phaselab.crispr.EnhancedGuide attribute) homopolymer (phaselab.crispr.EnhancedGuide attribute) I ibm_token (phaselab.quantum.QuantumConfig attribute) identify_target_enhancers() (in module phaselab.crispr) in_optimal_range (phaselab.crispr.GuidePair attribute) include_nogo (phaselab.crispr.EnhancedGuideConfig attribute) include_per_cry (phaselab.circadian.SMSClockParams attribute) index_guides_by_sequence() (in module phaselab.integrations.crispor) individual_score (phaselab.crispr.GuideCandidate attribute) individual_scores (phaselab.crispr.MultiEvidenceResult attribute) INSUFFICIENT_GUIDES (phaselab.crispr.DiscriminatorStatus attribute) integrate_crispor_offtargets() (in module phaselab.crispr) interaction_type (phaselab.crispr.GuidePair attribute) ir_analysis_done (phaselab.integrations.crispor.GuideCandidate attribute) ir_enhanced_score (phaselab.integrations.crispor.OffTargetIRAnalysis attribute) is_atlas_q_available() (in module phaselab.quantum) is_available() (phaselab.integrations.crispor.CrisporClient static method) is_canonical (phaselab.crispr.TSSAnnotation attribute) is_close (phaselab.integrations.crispor.OffTargetSite property) is_exonic (phaselab.integrations.crispor.OffTargetSite property) is_go (phaselab.crispr.EnhancedGuide property) (phaselab.crispr.MultiEvidenceResult attribute) (phaselab.crispr.QuantumGuideResult attribute) (phaselab.quantum.coherence.CoherenceResult attribute) is_go() (phaselab.crispr.BindingEnergyResult method) (phaselab.crispr.OffTargetGeometryResult method) (phaselab.crispr.PhaseAlignmentResult method) is_guide_coherent() (in module phaselab.crispr) (in module phaselab.crispr.coherence_utils) is_proximal (phaselab.crispr.Enhancer property) is_quantum_available() (phaselab.quantum.QuantumConfig method) is_quantum_measured (phaselab.integrations.crispor.CoherenceSource property) is_repeat (phaselab.crispr.CRISPORMetrics attribute) is_repeat_region() (in module phaselab.crispr) is_specific() (phaselab.crispr.OffTargetGeometryResult method) is_unknown (phaselab.crispr.EnhancedGuide attribute) is_viable (phaselab.crispr.EnhancedGuide property) J jet_lag_simulation() (in module phaselab.circadian) K K0 (phaselab.circadian.SMSClockParams attribute) K_base (phaselab.circadian.SMSClockParams attribute) K_global (phaselab.circadian.MultiTissueParams attribute) K_peripheral (phaselab.circadian.MultiTissueParams attribute) KNOCKOUT (phaselab.crispr.Modality attribute) knockout_window (phaselab.crispr.EnhancedGuideConfig attribute) KnockoutConfig (class in phaselab.crispr) kuramoto_ode() (in module phaselab.circadian) kuramoto_order_parameter() (in module phaselab.circadian) L largest_cluster_size (phaselab.integrations.crispor.OffTargetIRAnalysis attribute) layer_disagreements (phaselab.crispr.EnhancedGuide attribute) LBCAS12A (phaselab.crispr.Nuclease attribute) length (phaselab.crispr.Enhancer property) (phaselab.crispr.Region property) light_amplitude (phaselab.circadian.MultiTissueParams attribute) light_phase (phaselab.circadian.MultiTissueParams attribute) M manifest (phaselab.crispr.DesignResult attribute) (phaselab.crispr.DiscriminatorResult attribute) max_0mm (phaselab.crispr.PolicyConfig attribute) max_1mm (phaselab.crispr.PolicyConfig attribute) max_2mm (phaselab.crispr.PolicyConfig attribute) max_bystanders_in_window (phaselab.crispr.BaseEditConfig attribute) max_close_offtargets (phaselab.integrations.crispor.ScoringWeights attribute) max_enhancer_distance (phaselab.crispr.EnhancerConfig attribute) max_exonic_close_ot (phaselab.integrations.crispor.ScoringWeights attribute) max_gc (phaselab.crispr.BaseEditConfig attribute) (phaselab.crispr.CRISPRiConfig attribute) (phaselab.crispr.EnhancedGuideConfig attribute) (phaselab.crispr.GuideDesignConfig attribute) (phaselab.crispr.KnockoutConfig attribute) (phaselab.crispr.PrimeEditConfig attribute) max_guides (phaselab.crispr.MultiGuideConfig attribute) max_homopolymer (phaselab.crispr.BaseEditConfig attribute) (phaselab.crispr.CRISPRiConfig attribute) (phaselab.crispr.EnhancedGuideConfig attribute) (phaselab.crispr.GuideDesignConfig attribute) (phaselab.crispr.KnockoutConfig attribute) (phaselab.crispr.PrimeEditConfig attribute) max_homopolymer_run() (in module phaselab.crispr) max_interaction_distance (phaselab.crispr.MultiGuideConfig attribute) max_mismatches (phaselab.integrations.crispor.CrisporConfig attribute) max_offtargets (phaselab.crispr.EnhancedGuideConfig attribute) max_perfect_offtargets (phaselab.integrations.crispor.ScoringWeights attribute) max_score_unvalidated (phaselab.integrations.crispor.ScoringWeights attribute) max_secondary_structure_dg (phaselab.crispr.PrimeEditConfig attribute) max_spacing (phaselab.crispr.MultiGuideSet attribute) max_tail_risk (phaselab.integrations.crispor.ScoringWeights attribute) merge_crispor_data() (in module phaselab.integrations.crispor) method (phaselab.crispr.BindingEnergyResult attribute) (phaselab.quantum.coherence.CoherenceResult attribute) methylation (phaselab.crispr.EnhancedGuide attribute) min_abc_score (phaselab.crispr.EnhancerConfig attribute) min_activity_score (phaselab.crispr.EnhancerConfig attribute) min_coherence (phaselab.integrations.crispor.ScoringWeights attribute) min_complexity (phaselab.crispr.CRISPRiConfig attribute) (phaselab.crispr.EnhancedGuideConfig attribute) (phaselab.crispr.GuideDesignConfig attribute) (phaselab.crispr.KnockoutConfig attribute) min_cut_efficiency (phaselab.crispr.KnockoutConfig attribute) min_enhancer_length (phaselab.crispr.EnhancerConfig attribute) min_gc (phaselab.crispr.BaseEditConfig attribute) (phaselab.crispr.CRISPRiConfig attribute) (phaselab.crispr.EnhancedGuideConfig attribute) (phaselab.crispr.GuideDesignConfig attribute) (phaselab.crispr.KnockoutConfig attribute) (phaselab.crispr.PrimeEditConfig attribute) min_guides (phaselab.crispr.MultiGuideConfig attribute) min_mit_score (phaselab.integrations.crispor.ScoringWeights attribute) min_repression_efficiency (phaselab.crispr.CRISPRiConfig attribute) min_spacing (phaselab.crispr.MultiGuideConfig attribute) (phaselab.crispr.MultiGuideSet attribute) mismatch_positions (phaselab.integrations.crispor.CrisporOffTarget attribute) mismatches (phaselab.integrations.crispor.CrisporOffTarget attribute) (phaselab.integrations.crispor.OffTargetSite attribute) mit_score (phaselab.crispr.CRISPORMetrics attribute) (phaselab.crispr.EnhancedGuide attribute) mit_specificity (phaselab.integrations.crispor.CrisporGuideRow attribute) (phaselab.integrations.crispor.GuideCandidate attribute) mit_specificity_score() (in module phaselab.crispr) ml_confidence (phaselab.crispr.EnhancedGuide attribute) ml_efficiency (phaselab.crispr.EnhancedGuide attribute) ml_min_confidence (phaselab.crispr.EnhancedGuideConfig attribute) ml_predictors_used (phaselab.crispr.EnhancedGuide attribute) MM10 (phaselab.crispr.GenomeBuild attribute) MM39 (phaselab.crispr.GenomeBuild attribute) Modality (class in phaselab.crispr) modality (phaselab.crispr.DesignResult attribute) (phaselab.crispr.EnhancedGuideConfig attribute) (phaselab.crispr.Region attribute) (phaselab.crispr.RegionSet attribute) mode (phaselab.quantum.QuantumConfig attribute) module phaselab.circadian phaselab.core.coherence phaselab.core.constants phaselab.crispr phaselab.crispr.coherence_utils phaselab.integrations.crispor phaselab.quantum phaselab.quantum.coherence moreno_mateos (phaselab.integrations.crispor.CrisporGuideRow attribute) (phaselab.integrations.crispor.GuideCandidate attribute) MultiEvidenceResult (class in phaselab.crispr) MultiGuideConfig (class in phaselab.crispr) MultiGuideSet (class in phaselab.crispr) MultiTissueParams (class in phaselab.circadian) MultiTissueResult (class in phaselab.circadian) N n_clusters (phaselab.integrations.crispor.OffTargetIRAnalysis attribute) n_measurements (phaselab.quantum.coherence.CoherenceResult attribute) n_offtargets (phaselab.crispr.OffTargetGeometryResult attribute) n_offtargets_analyzed (phaselab.integrations.crispor.OffTargetIRAnalysis attribute) n_paulis (phaselab.crispr.BindingEnergyResult attribute) (phaselab.crispr.QuantumGuideResult attribute) n_qubits (phaselab.crispr.BindingEnergyResult attribute) (phaselab.crispr.QuantumGuideResult attribute) name (phaselab.crispr.Enhancer attribute) (phaselab.crispr.GuideCandidate attribute) (phaselab.crispr.NucleaseConfig attribute) (phaselab.crispr.PolicyConfig attribute) (phaselab.crispr.Window attribute) NO_DEGENERACY (phaselab.crispr.DiscriminatorStatus attribute) noise_strength (phaselab.circadian.MultiTissueParams attribute) (phaselab.circadian.SMSClockParams attribute) NOT_RUN (phaselab.crispr.DiscriminatorStatus attribute) Nuclease (class in phaselab.crispr) nuclease (phaselab.crispr.CandidateGuide attribute) (phaselab.crispr.DesignResult attribute) (phaselab.crispr.EnumerationResult attribute) NucleaseConfig (class in phaselab.crispr) NucleaseRole (class in phaselab.crispr) O OFF (phaselab.quantum.QuantumMode attribute) off_target_competitive (phaselab.integrations.crispor.OffTargetIRAnalysis attribute) off_targets (phaselab.crispr.CRISPORMetrics attribute) offtarget_count (phaselab.crispr.EnhancedGuide attribute) OffTargetGeometryResult (class in phaselab.crispr) OffTargetIRAnalysis (class in phaselab.integrations.crispor) offtargets_tsv (phaselab.integrations.crispor.CrisporOutput attribute) OffTargetSite (class in phaselab.integrations.crispor) omega_B (phaselab.circadian.SMSClockParams attribute) omega_C (phaselab.circadian.SMSClockParams attribute) optimal_guide_position() (in module phaselab.crispr) optimal_spacing_max (phaselab.crispr.MultiGuideConfig attribute) optimal_spacing_min (phaselab.crispr.MultiGuideConfig attribute) optimize_guide_spacing() (in module phaselab.crispr) ot_0mm (phaselab.integrations.crispor.CrisporGuideRow attribute) (phaselab.integrations.crispor.GuideCandidate attribute) ot_1mm (phaselab.integrations.crispor.CrisporGuideRow attribute) (phaselab.integrations.crispor.GuideCandidate attribute) ot_2mm (phaselab.integrations.crispor.CrisporGuideRow attribute) (phaselab.integrations.crispor.GuideCandidate attribute) ot_3mm (phaselab.integrations.crispor.CrisporGuideRow attribute) (phaselab.integrations.crispor.GuideCandidate attribute) ot_4mm (phaselab.integrations.crispor.CrisporGuideRow attribute) (phaselab.integrations.crispor.GuideCandidate attribute) ot_competitive (phaselab.integrations.crispor.GuideCandidate attribute) ot_energy_tail (phaselab.integrations.crispor.GuideCandidate attribute) ot_entropy (phaselab.integrations.crispor.GuideCandidate attribute) ot_entropy_normalized (phaselab.integrations.crispor.GuideCandidate attribute) ot_exonic_0mm (phaselab.integrations.crispor.CrisporGuideRow attribute) ot_exonic_1mm (phaselab.integrations.crispor.CrisporGuideRow attribute) ot_exonic_2mm (phaselab.integrations.crispor.CrisporGuideRow attribute) ot_exonic_3mm (phaselab.integrations.crispor.CrisporGuideRow attribute) ot_r_bar_max (phaselab.integrations.crispor.GuideCandidate attribute) out_of_frame (phaselab.integrations.crispor.CrisporGuideRow attribute) (phaselab.integrations.crispor.GuideCandidate attribute) output_dir (phaselab.integrations.crispor.CrisporOutput attribute) P P_init (phaselab.circadian.SMSClockParams attribute) pairs (phaselab.crispr.MultiGuideSet attribute) pam (phaselab.crispr.BaseEditConfig attribute) (phaselab.crispr.CandidateGuide attribute) (phaselab.crispr.CRISPRiConfig attribute) (phaselab.crispr.EnhancedGuide attribute) (phaselab.crispr.EnhancedGuideConfig attribute) (phaselab.crispr.GuideDesignConfig attribute) (phaselab.crispr.KnockoutConfig attribute) (phaselab.crispr.PrimeEditConfig attribute) (phaselab.integrations.crispor.CrisporConfig attribute) (phaselab.integrations.crispor.CrisporGuideRow attribute) (phaselab.integrations.crispor.GuideCandidate attribute) pam_display (phaselab.crispr.NucleaseConfig attribute) pam_display_binding (phaselab.crispr.NucleaseConfig attribute) pam_pattern (phaselab.crispr.NucleaseConfig attribute) pam_pattern_binding (phaselab.crispr.NucleaseConfig attribute) pam_side (phaselab.crispr.NucleaseConfig attribute) PAMScanner (class in phaselab.crispr) parse_guides_tsv() (in module phaselab.integrations.crispor) parse_offtargets_tsv() (in module phaselab.integrations.crispor) pass_rate (phaselab.crispr.BenchmarkResult attribute) passed (phaselab.crispr.BenchmarkResult attribute) (phaselab.crispr.GateResult attribute) passes_gates (phaselab.crispr.EnhancedGuide attribute) pbs_gc_max (phaselab.crispr.PrimeEditConfig attribute) pbs_gc_min (phaselab.crispr.PrimeEditConfig attribute) pbs_length_max (phaselab.crispr.PrimeEditConfig attribute) pbs_length_min (phaselab.crispr.PrimeEditConfig attribute) pbs_optimal_length (phaselab.crispr.PrimeEditConfig attribute) pbs_score() (in module phaselab.crispr) penalty_competitive_ot (phaselab.integrations.crispor.ScoringWeights attribute) penalty_concentrated_risk (phaselab.integrations.crispor.ScoringWeights attribute) penalty_exonic_close_ot (phaselab.integrations.crispor.ScoringWeights attribute) penalty_high_affinity_ot (phaselab.integrations.crispor.ScoringWeights attribute) penalty_per_close_ot (phaselab.integrations.crispor.ScoringWeights attribute) penalty_per_distant_ot (phaselab.integrations.crispor.ScoringWeights attribute) penalty_per_risk_mass_close (phaselab.integrations.crispor.ScoringWeights attribute) penalty_per_risk_mass_exonic (phaselab.integrations.crispor.ScoringWeights attribute) penalty_perfect_match_ot (phaselab.integrations.crispor.ScoringWeights attribute) penalty_tail_risk (phaselab.integrations.crispor.ScoringWeights attribute) phase_coherence (phaselab.crispr.PhaseAlignmentResult attribute) phase_concentration (phaselab.integrations.crispor.GuideCandidate attribute) phase_delays (phaselab.circadian.MultiTissueResult attribute) phase_mean (phaselab.integrations.crispor.GuideCandidate attribute) (phaselab.integrations.crispor.OffTargetSite attribute) phase_result (phaselab.crispr.MultiEvidenceResult attribute) phase_variance() (in module phaselab.core.coherence) phase_velocity (phaselab.crispr.PhaseAlignmentResult attribute) PhaseAlignmentResult (class in phaselab.crispr) phaselab.circadian module phaselab.core.coherence module phaselab.core.constants module phaselab.crispr module phaselab.crispr.coherence_utils module phaselab.integrations.crispor module phaselab.quantum module phaselab.quantum.coherence module phaselab_rankings (phaselab.crispr.BenchmarkResult attribute) phases (phaselab.circadian.MultiTissueResult attribute) policy (phaselab.crispr.DesignResult attribute) PolicyConfig (class in phaselab.crispr) poly_t_penalty() (in module phaselab.crispr) poly_t_threshold (phaselab.crispr.GuideDesignConfig attribute) position (phaselab.crispr.EnhancedGuide attribute) (phaselab.crispr.GuideCandidate attribute) (phaselab.crispr.TSSAnnotation attribute) (phaselab.integrations.crispor.GuideCandidate attribute) predict_enhancer_activation_effect() (in module phaselab.crispr) predict_pairwise_synergy() (in module phaselab.crispr) prefer_enhancer_center (phaselab.crispr.EnhancerConfig attribute) PRIME_EDITING (phaselab.crispr.Modality attribute) PrimeEditConfig (class in phaselab.crispr) print_ranking_report() (in module phaselab.crispr) published_guides (phaselab.crispr.BenchmarkResult attribute) python_bin (phaselab.integrations.crispor.CrisporConfig attribute) python_executable (phaselab.crispr.CrisporConfig attribute) Q QUANTUM (phaselab.crispr.coherence_utils.CoherenceMode attribute) (phaselab.crispr.CoherenceMode attribute) quantum_advantage (phaselab.crispr.DiscriminatorResult attribute) QUANTUM_FAILED (phaselab.crispr.DiscriminatorStatus attribute) quantum_status() (in module phaselab.quantum) QUANTUM_SUCCESS (phaselab.crispr.DiscriminatorStatus attribute) QuantumConfig (class in phaselab.quantum) QuantumGuideResult (class in phaselab.crispr) QuantumMode (class in phaselab.quantum) R r_bar (phaselab.integrations.crispor.GuideCandidate attribute) (phaselab.integrations.crispor.OffTargetSite attribute) R_bar (phaselab.quantum.coherence.CoherenceResult attribute) r_bar_off_max (phaselab.integrations.crispor.OffTargetIRAnalysis attribute) R_bar_off_mean (phaselab.crispr.OffTargetGeometryResult attribute) R_bar_off_std (phaselab.crispr.OffTargetGeometryResult attribute) R_bar_on (phaselab.crispr.OffTargetGeometryResult attribute) r_bar_on_target (phaselab.integrations.crispor.OffTargetIRAnalysis attribute) r_bar_std (phaselab.integrations.crispor.GuideCandidate attribute) r_bar_zscore (phaselab.integrations.crispor.GuideCandidate attribute) R_init (phaselab.circadian.SMSClockParams attribute) R_k (phaselab.circadian.SMSClockParams attribute) R_mid (phaselab.circadian.SMSClockParams attribute) R_target (phaselab.circadian.SMSClockParams attribute) rai1_scale_factor (phaselab.circadian.SMSClockParams attribute) rank (phaselab.integrations.crispor.GuideCandidate attribute) rank_guides() (in module phaselab.crispr) (in module phaselab.integrations.crispor) rank_guides_by_binding() (in module phaselab.crispr) rank_guides_by_geometry() (in module phaselab.crispr) rank_guides_by_phase() (in module phaselab.crispr) rank_guides_crispor_style() (in module phaselab.crispr) rank_guides_multi_evidence() (in module phaselab.crispr) ranked_guides (phaselab.crispr.DesignResult attribute) (phaselab.crispr.DiscriminatorResult attribute) RankingPolicy (class in phaselab.crispr) raw (phaselab.integrations.crispor.CrisporGuideRow attribute) reason (phaselab.crispr.GateResult attribute) recommendation (phaselab.crispr.EnhancerGuideResult attribute) (phaselab.crispr.MultiEvidenceResult attribute) (phaselab.crispr.MultiGuideSet attribute) REFSEQ (phaselab.crispr.TSSSource attribute) Region (class in phaselab.crispr) region (phaselab.integrations.crispor.OffTargetSite attribute) region_id (phaselab.crispr.CandidateGuide attribute) (phaselab.crispr.Region property) region_set (phaselab.crispr.DesignResult attribute) (phaselab.crispr.EnumerationResult attribute) RegionBuilder (class in phaselab.crispr) regions (phaselab.crispr.RegionSet attribute) RegionSet (class in phaselab.crispr) repair_pathway_prediction() (in module phaselab.crispr) repression_efficiency_score() (in module phaselab.crispr) repressor (phaselab.crispr.CRISPRiConfig attribute) require_tissue_match (phaselab.crispr.EnhancerConfig attribute) REQUIRED (phaselab.quantum.QuantumMode attribute) reverse_complement() (in module phaselab.crispr) risk_concentrated (phaselab.integrations.crispor.GuideCandidate attribute) (phaselab.integrations.crispor.OffTargetIRAnalysis attribute) risk_mass_close (phaselab.integrations.crispor.GuideCandidate attribute) risk_mass_distant (phaselab.integrations.crispor.GuideCandidate attribute) risk_mass_exonic (phaselab.integrations.crispor.GuideCandidate attribute) rt_length_max (phaselab.crispr.PrimeEditConfig attribute) rt_length_min (phaselab.crispr.PrimeEditConfig attribute) rt_optimal_length (phaselab.crispr.PrimeEditConfig attribute) rt_template_score() (in module phaselab.crispr) run_quantum_discriminator() (in module phaselab.crispr) S SACAS9 (phaselab.crispr.Nuclease attribute) save_results_json() (in module phaselab.integrations.crispor) scan_sequence() (phaselab.crispr.PAMScanner method) scn_peripheral_coherence (phaselab.circadian.MultiTissueResult attribute) score_breakdown (phaselab.integrations.crispor.GuideCandidate attribute) score_enhancer_for_activation() (in module phaselab.crispr) score_guides() (phaselab.integrations.crispor.CrisporClient method) score_sequence() (phaselab.integrations.crispor.CrisporClient method) ScoringWeights (class in phaselab.integrations.crispor) sequence (phaselab.crispr.CandidateGuide attribute) (phaselab.crispr.EnhancedGuide attribute) (phaselab.crispr.GuideCandidate attribute) (phaselab.integrations.crispor.CrisporGuideRow attribute) (phaselab.integrations.crispor.CrisporOffTarget attribute) (phaselab.integrations.crispor.GuideCandidate attribute) (phaselab.integrations.crispor.OffTargetSite attribute) sequence_with_pam (phaselab.crispr.CandidateGuide property) set_quantum_config() (in module phaselab.quantum) set_quantum_mode() (in module phaselab.quantum) setup_crispor() (in module phaselab.crispr) shift_work_simulation() (in module phaselab.circadian) shots (phaselab.quantum.QuantumConfig attribute) should_use_quantum() (phaselab.quantum.QuantumConfig method) significant_separations (phaselab.crispr.DiscriminatorResult attribute) simulate_multi_tissue() (in module phaselab.circadian) simulate_sms_clock() (in module phaselab.circadian) SMSClockParams (class in phaselab.circadian) source (phaselab.crispr.TSSAnnotation attribute) source_version (phaselab.crispr.TSSAnnotation attribute) spacing (phaselab.crispr.GuidePair attribute) SPCAS9 (phaselab.crispr.Nuclease attribute) SPCAS9_NG (phaselab.crispr.Nuclease attribute) specificity (phaselab.crispr.GuideCandidate attribute) specificity_score (phaselab.crispr.OffTargetGeometryResult attribute) stage1_pass (phaselab.integrations.crispor.GuideCandidate attribute) start (phaselab.crispr.CandidateGuide attribute) (phaselab.crispr.Enhancer attribute) (phaselab.crispr.Region attribute) (phaselab.integrations.crispor.CrisporGuideRow attribute) (phaselab.integrations.crispor.CrisporOffTarget attribute) status (phaselab.crispr.DiscriminatorResult attribute) stderr (phaselab.integrations.crispor.CrisporOutput attribute) stdout (phaselab.integrations.crispor.CrisporOutput attribute) steric_hindrance_score() (in module phaselab.crispr) strand (phaselab.crispr.CandidateGuide attribute) (phaselab.crispr.EnhancedGuide attribute) (phaselab.crispr.GuideCandidate attribute) (phaselab.crispr.Region attribute) (phaselab.crispr.TSSAnnotation attribute) (phaselab.integrations.crispor.CrisporGuideRow attribute) (phaselab.integrations.crispor.CrisporOffTarget attribute) (phaselab.integrations.crispor.GuideCandidate attribute) success (phaselab.integrations.crispor.CrisporOutput attribute) summary() (phaselab.crispr.BenchmarkResult method) (phaselab.crispr.DesignResult method) (phaselab.crispr.DiscriminatorResult method) (phaselab.crispr.EnhancedDesignResult method) (phaselab.crispr.EnumerationResult method) support_level (phaselab.crispr.TSSAnnotation attribute) synergy_factor (phaselab.crispr.MultiGuideSet attribute) synergy_model (phaselab.crispr.MultiGuideConfig attribute) synergy_score (phaselab.crispr.GuidePair attribute) T t (phaselab.circadian.MultiTissueResult attribute) tail_risk_score (phaselab.integrations.crispor.GuideCandidate attribute) target_base (phaselab.crispr.BaseEditConfig attribute) target_gene (phaselab.crispr.EnhancedDesignResult attribute) (phaselab.crispr.Enhancer attribute) target_gene_tss (phaselab.crispr.Enhancer attribute) target_tissue (phaselab.crispr.EnhancerConfig attribute) target_window (phaselab.crispr.KnockoutConfig attribute) tau_P (phaselab.circadian.SMSClockParams attribute) tau_R (phaselab.circadian.SMSClockParams attribute) tau_V (phaselab.circadian.SMSClockParams attribute) therapeutic_scan() (in module phaselab.circadian) tier_a_guides (phaselab.crispr.DesignResult property) tier_b_guides (phaselab.crispr.DesignResult property) tiers (phaselab.crispr.DesignResult attribute) timeout (phaselab.crispr.CrisporConfig attribute) (phaselab.integrations.crispor.CrisporConfig attribute) tissue (phaselab.crispr.Enhancer attribute) tissue_R_bars (phaselab.circadian.MultiTissueResult attribute) tissue_specific (phaselab.crispr.Enhancer attribute) tissues (phaselab.circadian.MultiTissueParams attribute) to_dataframe() (phaselab.crispr.DesignResult method) (phaselab.crispr.EnhancedDesignResult method) to_dict() (phaselab.circadian.MultiTissueResult method) (phaselab.crispr.CandidateGuide method) (phaselab.crispr.EnhancedGuide method) (phaselab.crispr.RegionSet method) (phaselab.integrations.crispor.GuideCandidate method) (phaselab.integrations.crispor.OffTargetIRAnalysis method) to_dict_list() (phaselab.crispr.EnumerationResult method) to_genomic() (phaselab.crispr.Window method) top_guide (phaselab.crispr.DesignResult property) top_n (phaselab.crispr.BaseEditConfig attribute) (phaselab.crispr.CRISPRiConfig attribute) (phaselab.crispr.EnhancedGuideConfig attribute) (phaselab.crispr.GuideDesignConfig attribute) (phaselab.crispr.KnockoutConfig attribute) (phaselab.crispr.PrimeEditConfig attribute) total_after_gates (phaselab.crispr.DesignResult attribute) total_candidates (phaselab.crispr.EnhancedDesignResult attribute) (phaselab.crispr.EnumerationResult property) total_close_offtargets (phaselab.integrations.crispor.CrisporGuideRow property) (phaselab.integrations.crispor.GuideCandidate property) total_enumerated (phaselab.crispr.DesignResult attribute) total_length (phaselab.crispr.RegionSet property) total_offtargets (phaselab.integrations.crispor.CrisporGuideRow attribute) (phaselab.integrations.crispor.GuideCandidate property) transcript_id (phaselab.crispr.TSSAnnotation attribute) tss_annotations (phaselab.crispr.RegionSet attribute) tss_id (phaselab.crispr.Region attribute) tss_position (phaselab.crispr.Region attribute) tss_relative_position (phaselab.crispr.CandidateGuide attribute) tss_source (phaselab.crispr.RegionSet attribute) tss_source_version (phaselab.crispr.RegionSet attribute) TSSAnnotation (class in phaselab.crispr) TSSSource (class in phaselab.crispr) U u6_compatibility_check() (in module phaselab.crispr) u6_compatible (phaselab.crispr.CRISPORMetrics attribute) UNKNOWN (phaselab.integrations.crispor.CoherenceSource attribute) upstream (phaselab.crispr.Window attribute) use_biological_context (phaselab.crispr.EnhancedGuideConfig attribute) use_default_window() (phaselab.crispr.RegionBuilder method) use_ml_predictors (phaselab.crispr.EnhancedGuideConfig attribute) V V_init (phaselab.circadian.SMSClockParams attribute) V_k (phaselab.circadian.SMSClockParams attribute) V_mid (phaselab.circadian.SMSClockParams attribute) V_phi (phaselab.quantum.coherence.CoherenceResult attribute) V_target (phaselab.circadian.SMSClockParams attribute) validate_and_rerank_with_crispor() (in module phaselab.crispr) validate_base_edit() (in module phaselab.crispr) validate_crispri_guide() (in module phaselab.crispr) validate_guide() (in module phaselab.crispr) validate_guide_set() (in module phaselab.crispr) validate_guides() (phaselab.crispr.CrisporValidator method) validate_knockout_guide() (in module phaselab.crispr) validate_prime_edit() (in module phaselab.crispr) validate_sequence() (phaselab.crispr.CrisporValidator method) validate_with_crispor() (in module phaselab.crispr) viable_guides (phaselab.crispr.EnhancedDesignResult property) vqe_iterations (phaselab.crispr.QuantumGuideResult attribute) W w_cfd (phaselab.integrations.crispor.ScoringWeights attribute) w_coherence (phaselab.integrations.crispor.ScoringWeights attribute) w_coherence_heuristic (phaselab.integrations.crispor.ScoringWeights attribute) w_doench (phaselab.integrations.crispor.ScoringWeights attribute) w_mit (phaselab.integrations.crispor.ScoringWeights attribute) warnings (phaselab.integrations.crispor.GuideCandidate attribute) weight_3mm (phaselab.crispr.PolicyConfig attribute) weight_4mm (phaselab.crispr.PolicyConfig attribute) weight_bystander (phaselab.crispr.BaseEditConfig attribute) weight_cfd (phaselab.crispr.BaseEditConfig attribute) (phaselab.crispr.CRISPRiConfig attribute) (phaselab.crispr.GuideDesignConfig attribute) (phaselab.crispr.KnockoutConfig attribute) (phaselab.crispr.PolicyConfig attribute) (phaselab.crispr.PrimeEditConfig attribute) weight_chromatin (phaselab.crispr.CRISPRiConfig attribute) (phaselab.crispr.GuideDesignConfig attribute) weight_coherence (phaselab.crispr.BaseEditConfig attribute) (phaselab.crispr.CRISPRiConfig attribute) (phaselab.crispr.GuideDesignConfig attribute) (phaselab.crispr.KnockoutConfig attribute) (phaselab.crispr.MultiGuideConfig attribute) (phaselab.crispr.PrimeEditConfig attribute) weight_context (phaselab.crispr.BaseEditConfig attribute) weight_cut_efficiency (phaselab.crispr.KnockoutConfig attribute) weight_delta_g (phaselab.crispr.CRISPRiConfig attribute) (phaselab.crispr.GuideDesignConfig attribute) (phaselab.crispr.KnockoutConfig attribute) weight_gc (phaselab.crispr.GuideDesignConfig attribute) weight_individual (phaselab.crispr.MultiGuideConfig attribute) weight_mit (phaselab.crispr.BaseEditConfig attribute) (phaselab.crispr.CRISPRiConfig attribute) (phaselab.crispr.GuideDesignConfig attribute) (phaselab.crispr.KnockoutConfig attribute) (phaselab.crispr.PolicyConfig attribute) (phaselab.crispr.PrimeEditConfig attribute) weight_nick_distance (phaselab.crispr.PrimeEditConfig attribute) weight_pbs_score (phaselab.crispr.PrimeEditConfig attribute) weight_position (phaselab.crispr.BaseEditConfig attribute) (phaselab.crispr.CRISPRiConfig attribute) weight_repression (phaselab.crispr.CRISPRiConfig attribute) weight_rt_score (phaselab.crispr.PrimeEditConfig attribute) weight_synergy (phaselab.crispr.MultiGuideConfig attribute) Window (class in phaselab.crispr) window (phaselab.crispr.EnhancedGuideConfig property) (phaselab.crispr.Region attribute) X X (phaselab.crispr.GuideTier attribute)
