Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W A ABLATION_VARIANTS (in module sctrial.benchmark.ablation) abundance_did() (in module sctrial.stats.abundance) add_block() (sctrial.benchmark.calibration.SummaryAccumulator method) add_effect_sizes_to_did() (in module sctrial.stats.effect_size) add_log1p_cpm_layer() (in module sctrial.preprocessing) (sctrial.workflow.TrialWorkflow method) add_qc_class_metrics() (in module sctrial.preprocessing) agg (sctrial.stats.did.DiDConfig attribute) aggregate (sctrial.stats.did.DiDConfig attribute) AggregateFunc (in module sctrial.stats.did) AggregateMode (in module sctrial.stats.did) ALPHA (in module sctrial.benchmark.endpoints) arm_bin() (sctrial.design.TrialDesign method) arm_col (sctrial.design.TrialDesign attribute) arm_control (sctrial.design.TrialDesign attribute) arm_treated (sctrial.design.TrialDesign attribute) assert_single_manifest() (in module sctrial.benchmark.manifest) auto_detect_design() (in module sctrial.convenience) B baseline_visit (sctrial.design.TrialDesign attribute) between_arm_comparison() (in module sctrial.stats.comparisons) build_params() (in module sctrial.benchmark.simulator_v2) build_scenario_grid() (in module sctrial.benchmark.orchestrator) build_sensitivity_grid() (in module sctrial.benchmark.orchestrator) C categorize_celltype() (in module sctrial.datasets) celltype_col (sctrial.design.TrialDesign attribute) check_covariate_balance() (in module sctrial.validation) check_did_assumptions() (in module sctrial.stats.diagnostics) check_scenario_results() (in module sctrial.benchmark.scenario_contract) check_simulation() (in module sctrial.benchmark.scenario_contract) cohens_d() (in module sctrial.stats.effect_size) cohens_d_from_did() (in module sctrial.stats.effect_size) cohens_d_from_did_approx() (in module sctrial.stats.effect_size) compare_fixed_vs_mixed() (in module sctrial.stats.mixed_effects) compare_gene_in_celltype() (in module sctrial.stats.comparisons) completed_scenarios() (sctrial.benchmark.paths.ResultLayout method) completion_marker() (sctrial.benchmark.paths.ResultLayout method) completion_record() (in module sctrial.benchmark.scenario_contract) composition_ablation() (in module sctrial.benchmark.gates) compute_bias_rmse() (in module sctrial.benchmark.metrics) compute_ci_coverage() (in module sctrial.benchmark.metrics) compute_failure_rates() (in module sctrial.benchmark.metrics) compute_fdr_tpr() (in module sctrial.benchmark.metrics) compute_fpr() (in module sctrial.benchmark.metrics) compute_lambda_gc() (in module sctrial.benchmark.metrics) compute_sign_recovery() (in module sctrial.benchmark.metrics) compute_topk_jaccard() (in module sctrial.benchmark.metrics) conditional_alpha() (sctrial.benchmark.calibration.SummaryAccumulator method) conditional_dispersion() (in module sctrial.benchmark.calibration) ContractReport (class in sctrial.benchmark.scenario_contract) CORE_METHODS (in module sctrial.benchmark) count_paired() (in module sctrial.datasets) covariates (sctrial.stats.did.DiDConfig attribute) crossover_col (sctrial.design.TrialDesign attribute) cv_summary() (in module sctrial.stats.cv) D design_effect() (in module sctrial.stats.power) diagnose_trial_data() (in module sctrial.validation) did_fit() (in module sctrial.stats.did) did_mixed() (in module sctrial.stats.mixed_effects) did_table() (in module sctrial.stats.did) (sctrial.workflow.TrialWorkflow method) did_table_bayes() (in module sctrial.stats.bayes) did_table_by_celltype() (in module sctrial.stats.did) did_table_mixed() (in module sctrial.stats.mixed_effects) did_table_parallel() (in module sctrial.stats.did) did_volcano_frame() (in module sctrial.plotting) DiDAnalyzer (class in sctrial.analysis) DiDConfig (class in sctrial.stats.did) DidFitResult (class in sctrial.stats.did) drop_artifact_genes() (in module sctrial.preprocessing) E e_value_rr() (in module sctrial.stats.sensitivity) effect_size_ci() (in module sctrial.stats.effect_size) effective_sample_size() (in module sctrial.stats.power) eligible_panel_genes() (in module sctrial.benchmark.simulator_v2) ensure_fdr() (in module sctrial.datasets) ensure_unique_index() (in module sctrial.utils) evaluability_by_method() (in module sctrial.benchmark.scenario_contract) event_study_did() (in module sctrial.stats.timeseries) exclude_artifacts_from_hvg() (in module sctrial.preprocessing) exclude_crossovers (sctrial.stats.did.DiDConfig attribute) expected_counts_per_cell() (in module sctrial.benchmark.simulator_v2) F fit() (sctrial.analysis.DiDAnalyzer method) flag_artifact_genes() (in module sctrial.preprocessing) followup_visit (sctrial.design.TrialDesign attribute) G GATE_STATISTICS (in module sctrial.benchmark.gates) GateResult (class in sctrial.benchmark.gates) gene_baseline_rates() (in module sctrial.benchmark.simulator_v2) genewise_corr_within_stratum() (sctrial.benchmark.calibration.SummaryAccumulator method) get_counts_matrix() (in module sctrial.utils) get_did_aggregated_df() (in module sctrial.stats.did) get_within_arm_aggregated_df() (in module sctrial.stats.comparisons) H harmonize_response() (in module sctrial.datasets) hazard_regression_with_features() (in module sctrial.stats.survival) hedges_g() (in module sctrial.stats.effect_size) I influence_diagnostics() (in module sctrial.stats.cv) intersect_preserve_order() (in module sctrial.utils) is_artifact_gene() (in module sctrial.preprocessing) iter_pv_blocks() (in module sctrial.benchmark.simulator_v2) K kfold_cv_did() (in module sctrial.stats.cv) L layer (sctrial.stats.did.DiDConfig attribute) load_aml() (in module sctrial.datasets) load_cart() (in module sctrial.datasets) load_empirical() (in module sctrial.benchmark.simulator_v2) load_sade_feldman() (in module sctrial.datasets) load_stephenson_data() (in module sctrial.datasets) load_tnbc_targets() (in module sctrial.benchmark.simulator_v2) load_tnbc_zhang() (in module sctrial.datasets) load_vaccine_gse171964() (in module sctrial.datasets) loo_cv_did() (in module sctrial.stats.cv) looks_like_counts() (in module sctrial.utils) M make_signal() (in module sctrial.benchmark) manifest_hash() (in module sctrial.benchmark.manifest) mc_max_for() (in module sctrial.benchmark.orchestrator) measure_targets() (in module sctrial.benchmark.calibration) METHOD_ESTIMAND (in module sctrial.benchmark) METHOD_INPUT (in module sctrial.benchmark) module sctrial.adata_tools sctrial.analysis sctrial.convenience sctrial.datasets sctrial.design sctrial.plotting sctrial.preprocessing sctrial.scoring sctrial.stats.abundance sctrial.stats.bayes sctrial.stats.comparisons sctrial.stats.cv sctrial.stats.diagnostics sctrial.stats.did sctrial.stats.effect_size sctrial.stats.gsea sctrial.stats.heterogeneity sctrial.stats.mixed_effects sctrial.stats.module_scores sctrial.stats.power sctrial.stats.pseudobulk sctrial.stats.sensitivity sctrial.stats.simulation sctrial.stats.summary sctrial.stats.survival sctrial.stats.timeseries sctrial.utils sctrial.validation sctrial.workflow module_score_did_by_pool() (in module sctrial.stats.module_scores) module_score_pseudobulk() (in module sctrial.stats.module_scores) module_score_within_arm_by_pool() (in module sctrial.stats.module_scores) N n_boot (sctrial.stats.did.DiDConfig attribute) nested_panels() (in module sctrial.benchmark) O oracle_estimands() (in module sctrial.benchmark) orphan_scenarios() (sctrial.benchmark.paths.ResultLayout method) P participant_col (sctrial.design.TrialDesign attribute) participant_log1p_cpm() (in module sctrial.benchmark.contracts) participant_sd (sctrial.benchmark.TranscriptomeSimConfig property) participant_visit_sd (sctrial.benchmark.TranscriptomeSimConfig property) permutation_pvalue() (in module sctrial.utils) permutation_pvalue_paired() (in module sctrial.utils) PINNED_STATISTICS (in module sctrial.benchmark.gates) plot_abundance_interaction() (in module sctrial.plotting) plot_did_forest() (in module sctrial.plotting) plot_did_forest_interactive() (in module sctrial.plotting) plot_did_volcano_interactive() (in module sctrial.plotting) plot_forest() (sctrial.analysis.DiDAnalyzer method) plot_gsea_heatmap() (in module sctrial.plotting) plot_gsea_radar() (in module sctrial.plotting) plot_module_umap_panel() (in module sctrial.plotting) plot_parallel_trends() (in module sctrial.plotting) plot_trial_dotplot() (in module sctrial.plotting) plot_trial_interaction() (in module sctrial.plotting) plot_trial_umap() (in module sctrial.plotting) plot_trial_umap_panel() (in module sctrial.plotting) plot_within_arm_comparison() (in module sctrial.plotting) polynomial_trend() (in module sctrial.stats.timeseries) power_curve() (in module sctrial.stats.power) power_did() (in module sctrial.stats.power) power_paired() (in module sctrial.stats.power) preflight_layout() (in module sctrial.benchmark.paths) prepare_inputs() (in module sctrial.benchmark) prepare_inputs_from_adata() (in module sctrial.benchmark.contracts) primary_visits() (sctrial.design.TrialDesign method) prior_predictive_check() (in module sctrial.stats.bayes) profile_features() (in module sctrial.adata_tools) pseudobulk_did() (in module sctrial.stats.pseudobulk) pseudobulk_export() (in module sctrial.stats.pseudobulk) pseudobulk_expression() (in module sctrial.stats.pseudobulk) pseudobulk_within_arm() (in module sctrial.stats.pseudobulk) publication_marker() (sctrial.benchmark.paths.ResultLayout method) pv_frame() (sctrial.benchmark.calibration.SummaryAccumulator method) Q Q_FDR (in module sctrial.benchmark.endpoints) quick_did() (in module sctrial.convenience) R replicate_endpoints() (in module sctrial.benchmark.endpoints) require_layout() (in module sctrial.benchmark.paths) required_cols() (sctrial.design.TrialDesign method) resolve_feature() (in module sctrial.utils) resolve_gene_name() (in module sctrial.stats.comparisons) result() (sctrial.workflow.TrialWorkflow method) ResultLayout (class in sctrial.benchmark.paths) run_ablation() (in module sctrial.benchmark.ablation) run_benchmark() (in module sctrial.benchmark) run_gates() (in module sctrial.benchmark.gates) run_gsea_cross_sectional() (in module sctrial.stats.gsea) run_gsea_did() (in module sctrial.stats.gsea) run_gsea_did_by_celltype() (in module sctrial.stats.gsea) run_gsea_did_multi() (in module sctrial.stats.gsea) run_gsea_pseudobulk() (in module sctrial.stats.gsea) run_gsea_within_arm() (in module sctrial.stats.gsea) run_method_comparison() (in module sctrial.stats.simulation) run_permutation_test() (in module sctrial.benchmark.permutation) run_sensitivity_benchmark() (in module sctrial.benchmark) run_subsampling() (in module sctrial.benchmark.subsample) S safe_filename() (in module sctrial.utils) sample_size_did() (in module sctrial.stats.power) sample_size_paired() (in module sctrial.stats.power) scenario_endpoints() (in module sctrial.benchmark.endpoints) scenario_seed() (in module sctrial.benchmark.orchestrator) scenarios_for() (sctrial.benchmark.paths.ResultLayout method) score_gene_sets() (in module sctrial.scoring) (sctrial.workflow.TrialWorkflow method) score_gene_sets_aucell() (in module sctrial.scoring) sctrial.adata_tools module sctrial.analysis module sctrial.convenience module sctrial.datasets module sctrial.design module sctrial.plotting module sctrial.preprocessing module sctrial.scoring module sctrial.stats.abundance module sctrial.stats.bayes module sctrial.stats.comparisons module sctrial.stats.cv module sctrial.stats.diagnostics module sctrial.stats.did module sctrial.stats.effect_size module sctrial.stats.gsea module sctrial.stats.heterogeneity module sctrial.stats.mixed_effects module sctrial.stats.module_scores module sctrial.stats.power module sctrial.stats.pseudobulk module sctrial.stats.sensitivity module sctrial.stats.simulation module sctrial.stats.summary module sctrial.stats.survival module sctrial.stats.timeseries module sctrial.utils module sctrial.validation module sctrial.workflow module seed (sctrial.stats.did.DiDConfig attribute) sensitivity_paired() (in module sctrial.stats.power) SEP (in module sctrial.benchmark.seeds) signed_logp() (in module sctrial.plotting) simulate_did_data() (in module sctrial.stats.simulation) simulate_trial_v2() (in module sctrial.benchmark) SOURCE_TREE_PATHS (in module sctrial.benchmark.manifest) source_tree_sha256() (in module sctrial.benchmark.manifest) stable_seed() (in module sctrial.benchmark.seeds) standardize (sctrial.stats.did.DiDConfig attribute) statistics() (sctrial.benchmark.calibration.SummaryAccumulator method) subset_cells() (in module sctrial.adata_tools) subset_primary() (in module sctrial.adata_tools) summarize() (sctrial.analysis.DiDAnalyzer method) summarize_adata() (in module sctrial.benchmark.calibration) summarize_blocks() (in module sctrial.benchmark.calibration) summarize_did_results() (in module sctrial.stats.summary) summarize_iteration() (in module sctrial.benchmark.metrics) summarize_simulation() (in module sctrial.benchmark.calibration) SummaryAccumulator (class in sctrial.benchmark.calibration) T test_parallel_trends() (in module sctrial.stats.timeseries) test_treatment_heterogeneity() (in module sctrial.stats.heterogeneity) TranscriptomeSimConfig (class in sctrial.benchmark) trend_interaction() (in module sctrial.stats.timeseries) TrialDataValidator (class in sctrial.validation) TrialDesign (class in sctrial.design) TrialWorkflow (class in sctrial.workflow) U use_bootstrap (sctrial.stats.did.DiDConfig attribute) V validate() (sctrial.design.TrialDesign method) validate_adata() (in module sctrial.validation) (sctrial.validation.TrialDataValidator static method) validate_features() (in module sctrial.validation) (sctrial.validation.TrialDataValidator static method) variance_components() (sctrial.benchmark.calibration.SummaryAccumulator method) verify_manifest() (in module sctrial.benchmark.manifest) verify_paired_participants() (in module sctrial.datasets) Violation (class in sctrial.benchmark.scenario_contract) visit_col (sctrial.design.TrialDesign attribute) W wild_cluster_bootstrap_t() (in module sctrial.utils) within_arm_comparison() (in module sctrial.stats.comparisons) within_arm_fit_beta() (in module sctrial.stats.comparisons) workflow() (in module sctrial.workflow)
