Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z _ __call__() (cellrank.kernels.utils.Correlation method) (cellrank.kernels.utils.Cosine method) (cellrank.kernels.utils.CustomThresholdScheme method) (cellrank.kernels.utils.DotProduct method) (cellrank.kernels.utils.HardThresholdScheme method) (cellrank.kernels.utils.SimilarityABC method) (cellrank.kernels.utils.SoftThresholdScheme method) (cellrank.kernels.utils.ThresholdSchemeABC method) A absorption_times (cellrank.estimators.CFLARE attribute) (cellrank.estimators.GPCCA attribute) adata (cellrank.estimators.CFLARE attribute) (cellrank.estimators.GPCCA attribute) (cellrank.kernels.BidirectionalKernel property) (cellrank.kernels.ConnectivityKernel attribute) (cellrank.kernels.CytoTRACEKernel attribute) (cellrank.kernels.Kernel property) (cellrank.kernels.PrecomputedKernel attribute) (cellrank.kernels.PseudotimeKernel attribute) (cellrank.kernels.RealTimeKernel attribute) (cellrank.kernels.UnidirectionalKernel property) (cellrank.kernels.VelocityKernel attribute) (cellrank.models.BaseModel property) (cellrank.models.GAM attribute) (cellrank.models.GAMR attribute) (cellrank.models.SKLearnModel attribute) aggregate_fate_probabilities() (in module cellrank.pl) B backward (cellrank.estimators.CFLARE attribute) (cellrank.estimators.GPCCA attribute) (cellrank.kernels.BidirectionalKernel property) (cellrank.kernels.ConnectivityKernel attribute) (cellrank.kernels.CytoTRACEKernel attribute) (cellrank.kernels.Kernel property) (cellrank.kernels.PrecomputedKernel attribute) (cellrank.kernels.PseudotimeKernel attribute) (cellrank.kernels.RealTimeKernel attribute) (cellrank.kernels.UnidirectionalKernel property) (cellrank.kernels.VelocityKernel attribute) BaseEstimator (class in cellrank.estimators) BaseModel (class in cellrank.models) bias_knn() (cellrank.kernels.utils.ThresholdSchemeABC method) BidirectionalKernel (class in cellrank.kernels) bone_marrow() (in module cellrank.datasets) C cbc() (cellrank.kernels.BidirectionalKernel method) (cellrank.kernels.ConnectivityKernel method) (cellrank.kernels.CytoTRACEKernel method) (cellrank.kernels.Kernel method) (cellrank.kernels.PrecomputedKernel method) (cellrank.kernels.PseudotimeKernel method) (cellrank.kernels.RealTimeKernel method) (cellrank.kernels.UnidirectionalKernel method) (cellrank.kernels.VelocityKernel method) cellrank module cellrank.datasets module cellrank.estimators module cellrank.kernels module cellrank.models module cellrank.pl module CFLARE (class in cellrank.estimators) circular_projection() (in module cellrank.pl) cluster_trends() (in module cellrank.pl) coarse_initial_distribution (cellrank.estimators.GPCCA attribute) coarse_stationary_distribution (cellrank.estimators.GPCCA attribute) coarse_T (cellrank.estimators.GPCCA attribute) colors (cellrank.Lineage property) compute_absorption_times() (cellrank.estimators.CFLARE method) (cellrank.estimators.GPCCA method) compute_coupling() (cellrank.kernels.RealTimeKernel method) compute_cytotrace() (cellrank.kernels.CytoTRACEKernel method) compute_eigendecomposition() (cellrank.estimators.CFLARE method) (cellrank.estimators.GPCCA method) compute_fate_probabilities() (cellrank.estimators.CFLARE method) (cellrank.estimators.GPCCA method) compute_lineage_drivers() (cellrank.estimators.CFLARE method) (cellrank.estimators.GPCCA method) compute_lineage_priming() (cellrank.estimators.CFLARE method) (cellrank.estimators.GPCCA method) compute_macrostates() (cellrank.estimators.GPCCA method) compute_schur() (cellrank.estimators.GPCCA method) compute_transition_matrix() (cellrank.kernels.BidirectionalKernel method) (cellrank.kernels.ConnectivityKernel method) (cellrank.kernels.CytoTRACEKernel method) (cellrank.kernels.Kernel method) (cellrank.kernels.PrecomputedKernel method) (cellrank.kernels.PseudotimeKernel method) (cellrank.kernels.RealTimeKernel method) (cellrank.kernels.UnidirectionalKernel method) (cellrank.kernels.VelocityKernel method) conf_int (cellrank.models.BaseModel property) (cellrank.models.GAM attribute) (cellrank.models.GAMR attribute) (cellrank.models.SKLearnModel attribute) confidence_interval() (cellrank.models.BaseModel method) (cellrank.models.GAM method) (cellrank.models.GAMR method) (cellrank.models.SKLearnModel method) connectivities (cellrank.kernels.ConnectivityKernel attribute) (cellrank.kernels.CytoTRACEKernel attribute) (cellrank.kernels.PseudotimeKernel attribute) (cellrank.kernels.VelocityKernel attribute) ConnectivityKernel (class in cellrank.kernels) copy() (cellrank.estimators.BaseEstimator method) (cellrank.estimators.CFLARE method) (cellrank.estimators.GPCCA method) (cellrank.kernels.BidirectionalKernel method) (cellrank.kernels.ConnectivityKernel method) (cellrank.kernels.CytoTRACEKernel method) (cellrank.kernels.Kernel method) (cellrank.kernels.PrecomputedKernel method) (cellrank.kernels.PseudotimeKernel method) (cellrank.kernels.RealTimeKernel method) (cellrank.kernels.UnidirectionalKernel method) (cellrank.kernels.VelocityKernel method) (cellrank.models.BaseModel method) (cellrank.models.GAM method) (cellrank.models.GAMR method) (cellrank.models.SKLearnModel method) Correlation (class in cellrank.kernels.utils) Cosine (class in cellrank.kernels.utils) couplings (cellrank.kernels.RealTimeKernel attribute) CustomThresholdScheme (class in cellrank.kernels.utils) CytoTRACEKernel (class in cellrank.kernels) D default_confidence_interval() (cellrank.models.BaseModel method) (cellrank.models.GAM method) (cellrank.models.GAMR method) (cellrank.models.SKLearnModel method) DotProduct (class in cellrank.kernels.utils) E eigendecomposition (cellrank.estimators.CFLARE attribute) (cellrank.estimators.GPCCA attribute) F fate_probabilities (cellrank.estimators.CFLARE attribute) (cellrank.estimators.GPCCA attribute) fit() (cellrank.estimators.BaseEstimator method) (cellrank.estimators.CFLARE method) (cellrank.estimators.GPCCA method) (cellrank.models.BaseModel method) (cellrank.models.GAM method) (cellrank.models.GAMR method) (cellrank.models.SKLearnModel method) from_adata() (cellrank.estimators.BaseEstimator class method) (cellrank.estimators.CFLARE class method) (cellrank.estimators.GPCCA class method) (cellrank.kernels.BidirectionalKernel class method) (cellrank.kernels.ConnectivityKernel class method) (cellrank.kernels.CytoTRACEKernel class method) (cellrank.kernels.Kernel class method) (cellrank.kernels.PrecomputedKernel class method) (cellrank.kernels.PseudotimeKernel class method) (cellrank.kernels.RealTimeKernel class method) (cellrank.kernels.UnidirectionalKernel class method) (cellrank.kernels.VelocityKernel class method) (cellrank.Lineage class method) from_moscot() (cellrank.kernels.RealTimeKernel class method) from_wot() (cellrank.kernels.RealTimeKernel class method) G GAM (class in cellrank.models) GAMR (class in cellrank.models) gene_trends() (in module cellrank.pl) GPCCA (class in cellrank.estimators) H HardThresholdScheme (class in cellrank.kernels.utils) heatmap() (in module cellrank.pl) hessian() (cellrank.kernels.utils.Correlation method) (cellrank.kernels.utils.Cosine method) (cellrank.kernels.utils.DotProduct method) I initial_states (cellrank.estimators.CFLARE attribute) (cellrank.estimators.GPCCA attribute) (cellrank.estimators.TermStatesEstimator property) initial_states_memberships (cellrank.estimators.GPCCA attribute) initial_states_probabilities (cellrank.estimators.CFLARE attribute) (cellrank.estimators.GPCCA attribute) (cellrank.estimators.TermStatesEstimator property) K kernel (cellrank.estimators.CFLARE attribute) (cellrank.estimators.GPCCA attribute) Kernel (class in cellrank.kernels) kernels (cellrank.kernels.BidirectionalKernel property) (cellrank.kernels.ConnectivityKernel attribute) (cellrank.kernels.CytoTRACEKernel attribute) (cellrank.kernels.Kernel property) (cellrank.kernels.PrecomputedKernel attribute) (cellrank.kernels.PseudotimeKernel attribute) (cellrank.kernels.RealTimeKernel attribute) (cellrank.kernels.UnidirectionalKernel property) (cellrank.kernels.VelocityKernel attribute) L Lineage (class in cellrank) lineage_drivers (cellrank.estimators.CFLARE attribute) (cellrank.estimators.GPCCA attribute) log_odds() (in module cellrank.pl) logits (cellrank.kernels.VelocityKernel attribute) lung() (in module cellrank.datasets) M macrostates (cellrank.estimators.GPCCA attribute) macrostates_memberships (cellrank.estimators.GPCCA attribute) model (cellrank.models.BaseModel property) (cellrank.models.GAM attribute) (cellrank.models.GAMR attribute) (cellrank.models.SKLearnModel attribute) module cellrank cellrank.datasets cellrank.estimators cellrank.kernels cellrank.models cellrank.pl N names (cellrank.Lineage property) O obs (cellrank.kernels.RealTimeKernel attribute) P pancreas() (in module cellrank.datasets) params (cellrank.estimators.BaseEstimator property) (cellrank.estimators.CFLARE attribute) (cellrank.estimators.GPCCA attribute) (cellrank.kernels.BidirectionalKernel property) (cellrank.kernels.ConnectivityKernel attribute) (cellrank.kernels.CytoTRACEKernel attribute) (cellrank.kernels.Kernel property) (cellrank.kernels.PrecomputedKernel attribute) (cellrank.kernels.PseudotimeKernel attribute) (cellrank.kernels.RealTimeKernel attribute) (cellrank.kernels.UnidirectionalKernel property) (cellrank.kernels.VelocityKernel attribute) plot() (cellrank.models.BaseModel method) (cellrank.models.GAM method) (cellrank.models.GAMR method) (cellrank.models.SKLearnModel method) plot_coarse_T() (cellrank.estimators.GPCCA method) plot_fate_probabilities() (cellrank.estimators.CFLARE method) (cellrank.estimators.GPCCA method) plot_lineage_drivers() (cellrank.estimators.CFLARE method) (cellrank.estimators.GPCCA method) plot_lineage_drivers_correlation() (cellrank.estimators.CFLARE method) (cellrank.estimators.GPCCA method) plot_macrostate_composition() (cellrank.estimators.GPCCA method) plot_macrostates() (cellrank.estimators.CFLARE method) (cellrank.estimators.GPCCA method) (cellrank.estimators.TermStatesEstimator method) plot_pie() (cellrank.Lineage method) plot_projection() (cellrank.kernels.BidirectionalKernel method) (cellrank.kernels.ConnectivityKernel method) (cellrank.kernels.CytoTRACEKernel method) (cellrank.kernels.Kernel method) (cellrank.kernels.PrecomputedKernel method) (cellrank.kernels.PseudotimeKernel method) (cellrank.kernels.RealTimeKernel method) (cellrank.kernels.UnidirectionalKernel method) (cellrank.kernels.VelocityKernel method) plot_random_walks() (cellrank.kernels.BidirectionalKernel method) (cellrank.kernels.ConnectivityKernel method) (cellrank.kernels.CytoTRACEKernel method) (cellrank.kernels.Kernel method) (cellrank.kernels.PrecomputedKernel method) (cellrank.kernels.PseudotimeKernel method) (cellrank.kernels.RealTimeKernel method) (cellrank.kernels.UnidirectionalKernel method) (cellrank.kernels.VelocityKernel method) plot_schur_matrix() (cellrank.estimators.GPCCA method) plot_single_flow() (cellrank.kernels.BidirectionalKernel method) (cellrank.kernels.ConnectivityKernel method) (cellrank.kernels.CytoTRACEKernel method) (cellrank.kernels.Kernel method) (cellrank.kernels.PrecomputedKernel method) (cellrank.kernels.PseudotimeKernel method) (cellrank.kernels.RealTimeKernel method) (cellrank.kernels.UnidirectionalKernel method) (cellrank.kernels.VelocityKernel method) plot_spectrum() (cellrank.estimators.CFLARE method) (cellrank.estimators.GPCCA method) plot_tsi() (cellrank.estimators.GPCCA method) PrecomputedKernel (class in cellrank.kernels) predict() (cellrank.estimators.BaseEstimator method) (cellrank.estimators.CFLARE method) (cellrank.estimators.GPCCA method) (cellrank.models.BaseModel method) (cellrank.models.GAM method) (cellrank.models.GAMR method) (cellrank.models.SKLearnModel method) predict_initial_states() (cellrank.estimators.GPCCA method) predict_terminal_states() (cellrank.estimators.GPCCA method) prepare() (cellrank.models.BaseModel method) (cellrank.models.GAM method) (cellrank.models.GAMR method) (cellrank.models.SKLearnModel method) prepared (cellrank.models.BaseModel property) (cellrank.models.GAM attribute) (cellrank.models.GAMR attribute) (cellrank.models.SKLearnModel attribute) priming_degree (cellrank.estimators.CFLARE attribute) (cellrank.estimators.GPCCA attribute) priming_degree() (cellrank.Lineage method) pseudotime (cellrank.kernels.CytoTRACEKernel attribute) (cellrank.kernels.PseudotimeKernel attribute) PseudotimeKernel (class in cellrank.kernels) R read() (cellrank.estimators.CFLARE static method) (cellrank.estimators.GPCCA static method) (cellrank.kernels.BidirectionalKernel static method) (cellrank.kernels.ConnectivityKernel static method) (cellrank.kernels.CytoTRACEKernel static method) (cellrank.kernels.Kernel static method) (cellrank.kernels.PrecomputedKernel static method) (cellrank.kernels.PseudotimeKernel static method) (cellrank.kernels.RealTimeKernel static method) (cellrank.kernels.UnidirectionalKernel static method) (cellrank.kernels.VelocityKernel static method) (cellrank.models.GAM static method) (cellrank.models.GAMR static method) (cellrank.models.SKLearnModel static method) RealTimeKernel (class in cellrank.kernels) reduce() (cellrank.Lineage method) rename_initial_states() (cellrank.estimators.CFLARE method) (cellrank.estimators.GPCCA method) (cellrank.estimators.TermStatesEstimator method) rename_terminal_states() (cellrank.estimators.CFLARE method) (cellrank.estimators.GPCCA method) (cellrank.estimators.TermStatesEstimator method) reprogramming_morris() (in module cellrank.datasets) reprogramming_schiebinger() (in module cellrank.datasets) S schur_matrix (cellrank.estimators.GPCCA attribute) schur_vectors (cellrank.estimators.GPCCA attribute) set_initial_states() (cellrank.estimators.CFLARE method) (cellrank.estimators.GPCCA method) (cellrank.estimators.TermStatesEstimator method) set_terminal_states() (cellrank.estimators.CFLARE method) (cellrank.estimators.GPCCA method) (cellrank.estimators.TermStatesEstimator method) shape (cellrank.estimators.CFLARE attribute) (cellrank.estimators.GPCCA attribute) (cellrank.kernels.BidirectionalKernel property) (cellrank.kernels.ConnectivityKernel attribute) (cellrank.kernels.CytoTRACEKernel attribute) (cellrank.kernels.Kernel property) (cellrank.kernels.PrecomputedKernel attribute) (cellrank.kernels.PseudotimeKernel attribute) (cellrank.kernels.RealTimeKernel attribute) (cellrank.kernels.UnidirectionalKernel property) (cellrank.kernels.VelocityKernel attribute) (cellrank.models.BaseModel property) (cellrank.models.GAM attribute) (cellrank.models.GAMR attribute) (cellrank.models.SKLearnModel attribute) SimilarityABC (class in cellrank.kernels.utils) SKLearnModel (class in cellrank.models) SoftThresholdScheme (class in cellrank.kernels.utils) T T (cellrank.Lineage property) terminal_states (cellrank.estimators.CFLARE attribute) (cellrank.estimators.GPCCA attribute) (cellrank.estimators.TermStatesEstimator property) terminal_states_memberships (cellrank.estimators.GPCCA attribute) terminal_states_probabilities (cellrank.estimators.CFLARE attribute) (cellrank.estimators.GPCCA attribute) (cellrank.estimators.TermStatesEstimator property) TermStatesEstimator (class in cellrank.estimators) ThresholdSchemeABC (class in cellrank.kernels.utils) time (cellrank.kernels.RealTimeKernel attribute) to_adata() (cellrank.estimators.BaseEstimator method) (cellrank.estimators.CFLARE method) (cellrank.estimators.GPCCA method) transition_matrix (cellrank.estimators.CFLARE attribute) (cellrank.estimators.GPCCA attribute) (cellrank.kernels.BidirectionalKernel property) (cellrank.kernels.ConnectivityKernel attribute) (cellrank.kernels.CytoTRACEKernel attribute) (cellrank.kernels.Kernel property) (cellrank.kernels.PrecomputedKernel attribute) (cellrank.kernels.PseudotimeKernel attribute) (cellrank.kernels.RealTimeKernel attribute) (cellrank.kernels.UnidirectionalKernel property) (cellrank.kernels.VelocityKernel attribute) tsi() (cellrank.estimators.GPCCA method) U UnidirectionalKernel (class in cellrank.kernels) V VelocityKernel (class in cellrank.kernels) view() (cellrank.Lineage method) W w (cellrank.models.BaseModel property) (cellrank.models.GAM attribute) (cellrank.models.GAMR attribute) (cellrank.models.SKLearnModel attribute) w_all (cellrank.models.BaseModel property) (cellrank.models.GAM attribute) (cellrank.models.GAMR attribute) (cellrank.models.SKLearnModel attribute) write() (cellrank.estimators.CFLARE method) (cellrank.estimators.GPCCA method) (cellrank.kernels.BidirectionalKernel method) (cellrank.kernels.ConnectivityKernel method) (cellrank.kernels.CytoTRACEKernel method) (cellrank.kernels.Kernel method) (cellrank.kernels.PrecomputedKernel method) (cellrank.kernels.PseudotimeKernel method) (cellrank.kernels.RealTimeKernel method) (cellrank.kernels.UnidirectionalKernel method) (cellrank.kernels.VelocityKernel method) (cellrank.models.GAM method) (cellrank.models.GAMR method) (cellrank.models.SKLearnModel method) write_to_adata() (cellrank.kernels.BidirectionalKernel method) (cellrank.kernels.ConnectivityKernel method) (cellrank.kernels.CytoTRACEKernel method) (cellrank.kernels.Kernel method) (cellrank.kernels.PrecomputedKernel method) (cellrank.kernels.PseudotimeKernel method) (cellrank.kernels.RealTimeKernel method) (cellrank.kernels.UnidirectionalKernel method) (cellrank.kernels.VelocityKernel method) X X (cellrank.Lineage property) x (cellrank.models.BaseModel property) (cellrank.models.GAM attribute) (cellrank.models.GAMR attribute) (cellrank.models.SKLearnModel attribute) x_all (cellrank.models.BaseModel property) (cellrank.models.GAM attribute) (cellrank.models.GAMR attribute) (cellrank.models.SKLearnModel attribute) x_hat (cellrank.models.BaseModel property) (cellrank.models.GAM attribute) (cellrank.models.GAMR attribute) (cellrank.models.SKLearnModel attribute) x_test (cellrank.models.BaseModel property) (cellrank.models.GAM attribute) (cellrank.models.GAMR attribute) (cellrank.models.SKLearnModel attribute) Y y (cellrank.models.BaseModel property) (cellrank.models.GAM attribute) (cellrank.models.GAMR attribute) (cellrank.models.SKLearnModel attribute) y_all (cellrank.models.BaseModel property) (cellrank.models.GAM attribute) (cellrank.models.GAMR attribute) (cellrank.models.SKLearnModel attribute) y_hat (cellrank.models.BaseModel property) (cellrank.models.GAM attribute) (cellrank.models.GAMR attribute) (cellrank.models.SKLearnModel attribute) y_test (cellrank.models.BaseModel property) (cellrank.models.GAM attribute) (cellrank.models.GAMR attribute) (cellrank.models.SKLearnModel attribute) Z zebrafish() (in module cellrank.datasets)