Index A | C | D | E | F | G | L | M | N | O | P | R | S | T | V | W A added_genes (circust.top_genes.TopGeneResult attribute) assign_sectors() (in module circust.top_genes) C candidate_matrix (circust.top_genes.TopGeneResult attribute) circular_median() (in module circust.top_genes) circular_scale (circust.cpca.CPCAResult attribute) (circust.robust_order.RobustOrderResult attribute) (circust.synchronizer.SynchronizationResult attribute) (circust.top_genes.TopGeneResult attribute) circular_scales (circust.robust_order.RobustOrderResult attribute) circular_unimodal_fit() (in module circust.fitting.ori) CircularSynchronizer (class in circust.synchronizer) circust.core_genes module circust.cpca module circust.fitting.cosinor module circust.fitting.fmm module circust.fitting.ori module circust.fitting.rhythm_model module circust.preprocessing module circust.robust_order module circust.synchronizer module circust.top_genes module circust.visualization.cpca_plots module circust.visualization.order_plots module circust.visualization.outlier_plots module circust.visualization.pipeline_summary module core_genes (circust.synchronizer.SynchronizationResult attribute) core_genes_found (circust.cpca.CPCAResult attribute) core_norm_final (circust.cpca.CPCAResult attribute) CoreGeneResult (class in circust.core_genes) CoreGeneSelector (class in circust.core_genes) cosinor_fits_initial (circust.cpca.CPCAResult attribute) cosinor_peaks (circust.top_genes.TopGeneResult attribute) CosinorModel (class in circust.fitting.cosinor) CPCA (class in circust.cpca) CPCAResult (class in circust.cpca) D day_genes (circust.synchronizer.SynchronizationResult attribute) direction_flipped (circust.robust_order.RobustOrderResult attribute) (circust.synchronizer.SynchronizationResult attribute) dropped_duplicates (circust.preprocessing.PreprocessingResult attribute) dropped_sparse (circust.preprocessing.PreprocessingResult attribute) E expr_norm (circust.preprocessing.PreprocessingResult attribute) expr_norm_final (circust.cpca.CPCAResult attribute) expr_ordered (circust.synchronizer.SynchronizationResult attribute) expr_raw (circust.preprocessing.PreprocessingResult attribute) F fallback_used (circust.robust_order.RobustOrderResult attribute) find_local_extrema() (in module circust.fitting.ori) fit() (circust.fitting.cosinor.CosinorModel method) (circust.fitting.fmm.FMMModel method) (circust.fitting.ori.ORIModel method) (circust.fitting.rhythm_model.RhythmModel method) FitResult (class in circust.fitting.rhythm_model) fitted (circust.fitting.rhythm_model.FitResult attribute) fmm_fits_final (circust.cpca.CPCAResult attribute) fmm_fits_initial (circust.cpca.CPCAResult attribute) fmm_outliers (circust.cpca.CPCAResult attribute) fmm_params (circust.synchronizer.SynchronizationResult attribute) fmm_peak_times_final (circust.cpca.CPCAResult attribute) fmm_peaks (circust.top_genes.TopGeneResult attribute) FMMModel (class in circust.fitting.fmm) from_string() (circust.core_genes.CoreGeneSelector class method) G gene_names (circust.top_genes.TopGeneResult attribute) genes (circust.core_genes.CoreGeneResult attribute) genes_requested (circust.core_genes.CoreGeneResult attribute) L load_expression_matrix() (in module circust.preprocessing) M median_r2_per_rep (circust.robust_order.RobustOrderResult attribute) method_used (circust.robust_order.RobustOrderResult attribute) missing (circust.core_genes.CoreGeneResult attribute) model_name (circust.fitting.rhythm_model.FitResult attribute) module circust.core_genes circust.cpca circust.fitting.cosinor circust.fitting.fmm circust.fitting.ori circust.fitting.rhythm_model circust.preprocessing circust.robust_order circust.synchronizer circust.top_genes circust.visualization.cpca_plots circust.visualization.order_plots circust.visualization.outlier_plots circust.visualization.pipeline_summary N n_after_fmm (circust.top_genes.TopGeneResult attribute) n_after_ori (circust.top_genes.TopGeneResult attribute) n_attempts (circust.robust_order.RobustOrderResult attribute) n_genes_in (circust.preprocessing.PreprocessingResult attribute) n_genes_out (circust.preprocessing.PreprocessingResult attribute) n_samples (circust.preprocessing.PreprocessingResult attribute) n_total_genes (circust.top_genes.TopGeneResult attribute) night_genes (circust.synchronizer.SynchronizationResult attribute) normalise_matrix() (in module circust.preprocessing) O omega (circust.top_genes.TopGeneResult attribute) ORIModel (class in circust.fitting.ori) P params (circust.fitting.rhythm_model.FitResult attribute) pava_decreasing() (in module circust.fitting.ori) pava_increasing() (in module circust.fitting.ori) pc1 (circust.cpca.CPCAResult attribute) pc1_initial (circust.cpca.CPCAResult attribute) pc2 (circust.cpca.CPCAResult attribute) pc2_initial (circust.cpca.CPCAResult attribute) pc3 (circust.cpca.CPCAResult attribute) peak_time (circust.fitting.rhythm_model.FitResult attribute) peak_time() (circust.fitting.cosinor.CosinorModel static method) (circust.fitting.fmm.FMMModel static method) (circust.fitting.ori.ORIModel static method) peak_times (circust.synchronizer.SynchronizationResult attribute) per_rep_cos_fit (circust.robust_order.RobustOrderResult attribute) per_rep_fmm_fit (circust.robust_order.RobustOrderResult attribute) per_rep_np_fit (circust.robust_order.RobustOrderResult attribute) plot_circular_peaks() (in module circust.visualization.order_plots) plot_core_gene_fits() (in module circust.visualization.outlier_plots) plot_day_night_diagram() (in module circust.visualization.order_plots) plot_expression_overview() (in module circust.visualization.pipeline_summary) plot_gene_panels() (in module circust.visualization.cpca_plots) plot_ordered_profiles() (in module circust.visualization.order_plots) plot_pc_scatter() (in module circust.visualization.cpca_plots) plot_pipeline_summary() (in module circust.visualization.pipeline_summary) plot_r2_comparison() (in module circust.visualization.order_plots) plot_residual_heatmap() (in module circust.visualization.outlier_plots) plot_residual_strips() (in module circust.visualization.outlier_plots) plot_variance_explained() (in module circust.visualization.pipeline_summary) pre_circular_scale (circust.synchronizer.SynchronizationResult attribute) pre_direction_reversed (circust.synchronizer.SynchronizationResult attribute) pre_expr_ordered (circust.synchronizer.SynchronizationResult attribute) pre_fmm_params (circust.synchronizer.SynchronizationResult attribute) pre_peak_times (circust.synchronizer.SynchronizationResult attribute) pre_sample_order (circust.synchronizer.SynchronizationResult attribute) PreprocessingResult (class in circust.preprocessing) Preprocessor (class in circust.preprocessing) preset (circust.core_genes.CoreGeneResult attribute) PRESETS (circust.core_genes.CoreGeneSelector attribute) R r2 (circust.fitting.rhythm_model.FitResult attribute) r2_fmm (circust.synchronizer.SynchronizationResult attribute) r2_ori (circust.top_genes.TopGeneResult attribute) r2_par (circust.top_genes.TopGeneResult attribute) residuals (circust.fitting.rhythm_model.FitResult attribute) residuals_std (circust.fitting.rhythm_model.FitResult attribute) RhythmModel (class in circust.fitting.rhythm_model) RobustOrderEstimator (class in circust.robust_order) RobustOrderResult (class in circust.robust_order) run() (circust.cpca.CPCA method) (circust.preprocessing.Preprocessor method) (circust.robust_order.RobustOrderEstimator method) (circust.synchronizer.CircularSynchronizer method) (circust.top_genes.TopGeneSelector method) S sample_order (circust.cpca.CPCAResult attribute) (circust.robust_order.RobustOrderResult attribute) (circust.synchronizer.SynchronizationResult attribute) (circust.top_genes.TopGeneResult attribute) sample_orders (circust.robust_order.RobustOrderResult attribute) samples_dropped (circust.cpca.CPCAResult attribute) sector_boundaries() (in module circust.top_genes) sector_centres (circust.top_genes.TopGeneResult attribute) sector_labels (circust.top_genes.TopGeneResult attribute) select() (circust.core_genes.CoreGeneSelector method) selected_rep (circust.robust_order.RobustOrderResult attribute) selection_names (circust.robust_order.RobustOrderResult attribute) selection_score (circust.robust_order.RobustOrderResult attribute) sse (circust.fitting.rhythm_model.FitResult attribute) stats_table (circust.robust_order.RobustOrderResult attribute) std_residuals_fmm (circust.cpca.CPCAResult attribute) summary() (circust.core_genes.CoreGeneResult method) (circust.cpca.CPCAResult method) (circust.fitting.rhythm_model.FitResult method) (circust.preprocessing.PreprocessingResult method) (circust.robust_order.RobustOrderResult method) (circust.synchronizer.SynchronizationResult method) (circust.top_genes.TopGeneResult method) SynchronizationResult (class in circust.synchronizer) T top_gene_names (circust.robust_order.RobustOrderResult attribute) TopGeneResult (class in circust.top_genes) TopGeneSelector (class in circust.top_genes) V variance_explained (circust.cpca.CPCAResult attribute) W within_group_indices (circust.synchronizer.SynchronizationResult attribute)