Index

A

adata (scCS.multicomparison.MultiScorer attribute) (scCS.pairwise.PairScorer attribute) adata_sub (scCS.multicomparison.MultiScorer property) (scCS.MultiScorer property) (scCS.PairScorer property) (scCS.pairwise.PairScorer property)

arm_angles_deg (scCS.bifurcation.FateMap attribute), [1] (scCS.FateMap attribute), [1]

B

bin_angles() (in module scCS) (in module scCS.scores) bin_edges (scCS.CommitmentScoreResult attribute), [1] (scCS.scores.CommitmentScoreResult attribute), [1] bootstrap_ci (scCS.CommitmentScoreResult attribute) (scCS.scores.CommitmentScoreResult attribute) bootstrap_cs() (in module scCS) (in module scCS.scores) branches (scCS.multicomparison.MultiScorer attribute) (scCS.pairwise.PairScorer attribute)

build_embedding() (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method) (scCS.PairScorer method) (scCS.pairwise.PairScorer method) build_fate_map() (in module scCS) (in module scCS.bifurcation) build_star_embedding() (in module scCS) (in module scCS.embedding)

C

cell_obs_names (scCS.CommitmentScoreResult attribute) (scCS.scores.CommitmentScoreResult attribute) cell_scores (scCS.CommitmentScoreResult attribute), [1] (scCS.scores.CommitmentScoreResult attribute), [1] centroid_sectors() (in module scCS) (in module scCS.scores) commitment_entropy (scCS.CommitmentScoreResult property) (scCS.scores.CommitmentScoreResult property) commitment_vector (scCS.CommitmentScoreResult attribute), [1] (scCS.scores.CommitmentScoreResult attribute), [1] CommitmentScoreResult (class in scCS) (class in scCS.scores) compare_conditions() (scCS.PairScorer method) (scCS.pairwise.PairScorer method) compare_omnibus() (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method) compare_posthoc() (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method) compute_angles() (in module scCS) (in module scCS.scores) compute_cell_scores() (in module scCS) (in module scCS.scores) compute_commitment_entropy (in module scCS.scores) compute_commitment_vector() (in module scCS) (in module scCS.scores) compute_delta_CS() (scCS.PairScorer method) (scCS.pairwise.PairScorer method) compute_local_pseudotime() (in module scCS) (in module scCS.embedding)

compute_magnitudes() (in module scCS) (in module scCS.scores) compute_mean_cell_entropy() (in module scCS) (in module scCS.scores) compute_nCS() (in module scCS) (in module scCS.scores) compute_nn_cell_entropy() (in module scCS) (in module scCS.scores) compute_pairwise_cs_matrix() (in module scCS) (in module scCS.scores) compute_pairwise_deltas() (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method) compute_per_fate_cell_entropy() (in module scCS) (in module scCS.scores) compute_population_entropy() (in module scCS) (in module scCS.scores) compute_sector_magnitudes() (in module scCS) (in module scCS.scores) compute_unCS() (in module scCS) (in module scCS.scores) compute_velocity() (scCS.single.SingleScorer method) (scCS.SingleScorer method) condition_obs_key (scCS.multicomparison.MultiScorer attribute) (scCS.pairwise.PairScorer attribute) CONDITION_PALETTE (in module scCS.plot) conditions (scCS.multicomparison.MultiScorer attribute) (scCS.pairwise.PairScorer attribute)

D

dominant_fate (scCS.CommitmentScoreResult attribute) (scCS.CommitmentScoreResult property) (scCS.scores.CommitmentScoreResult attribute) (scCS.scores.CommitmentScoreResult property)

E

equal_sectors() (in module scCS) (in module scCS.scores)

export_enrichment_tables() (in module scCS) (in module scCS.enrichment)

F

fate_angles (scCS.CommitmentScoreResult attribute), [1] (scCS.scores.CommitmentScoreResult attribute), [1] fate_cell_indices (scCS.bifurcation.FateMap attribute), [1] (scCS.FateMap attribute), [1] fate_centroids (scCS.bifurcation.FateMap attribute), [1] (scCS.FateMap attribute), [1] fate_names (scCS.bifurcation.FateMap attribute), [1] (scCS.CommitmentScoreResult attribute), [1] (scCS.FateMap attribute), [1] (scCS.scores.CommitmentScoreResult attribute), [1] FATE_PALETTE (in module scCS.plot) FateMap (class in scCS) (class in scCS.bifurcation)

fit() (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method) (scCS.PairScorer method) (scCS.pairwise.PairScorer method) (scCS.single.SingleScorer method) (scCS.SingleScorer method) fit_mixed_model() (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method) (scCS.PairScorer method) (scCS.pairwise.PairScorer method) fit_mixed_model_contrasts() (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method)

G

get_deg_drivers() (in module scCS) (in module scCS.drivers) (scCS.single.SingleScorer method) (scCS.SingleScorer method) get_enrichment() (scCS.single.SingleScorer method) (scCS.SingleScorer method) get_velocity_drivers() (in module scCS) (in module scCS.drivers) (scCS.single.SingleScorer method) (scCS.SingleScorer method)

get_velocity_fate_drivers() (in module scCS) (in module scCS.drivers) (scCS.single.SingleScorer method) (scCS.SingleScorer method)

I

is_fitted (scCS.multicomparison.MultiScorer property) (scCS.MultiScorer property) (scCS.PairScorer property) (scCS.pairwise.PairScorer property)

K

k (scCS.bifurcation.FateMap attribute) (scCS.bifurcation.FateMap property) (scCS.CommitmentScoreResult property) (scCS.FateMap attribute) (scCS.FateMap property) (scCS.scores.CommitmentScoreResult property)

L

load() (scCS.single.SingleScorer class method) (scCS.SingleScorer class method)

M

M_bin (scCS.CommitmentScoreResult attribute), [1] (scCS.scores.CommitmentScoreResult attribute), [1] M_sector (scCS.CommitmentScoreResult attribute), [1] (scCS.scores.CommitmentScoreResult attribute), [1] mean_cell_entropy (scCS.CommitmentScoreResult attribute), [1] (scCS.scores.CommitmentScoreResult attribute), [1] module scCS scCS.bifurcation scCS.drivers scCS.embedding scCS.enrichment scCS.multicomparison scCS.pairwise scCS.plot scCS.scores scCS.single

MultiScorer (class in scCS) (class in scCS.multicomparison)

N

n_angle_bins (scCS.multicomparison.MultiScorer attribute) (scCS.pairwise.PairScorer attribute) n_cells_per_fate (scCS.CommitmentScoreResult attribute), [1] (scCS.scores.CommitmentScoreResult attribute), [1]

nn_cell_entropy (scCS.CommitmentScoreResult attribute), [1] (scCS.scores.CommitmentScoreResult attribute), [1] nn_k (scCS.CommitmentScoreResult attribute), [1] (scCS.scores.CommitmentScoreResult attribute), [1]

O

obs_key (scCS.bifurcation.FateMap attribute), [1] (scCS.FateMap attribute), [1] (scCS.multicomparison.MultiScorer attribute) (scCS.pairwise.PairScorer attribute)

P

PairScorer (class in scCS) (class in scCS.pairwise) pairwise_nCS (scCS.CommitmentScoreResult attribute), [1] (scCS.scores.CommitmentScoreResult attribute), [1] pairwise_to_dataframe() (scCS.CommitmentScoreResult method) (scCS.scores.CommitmentScoreResult method) pairwise_unCS (scCS.CommitmentScoreResult attribute), [1] (scCS.scores.CommitmentScoreResult attribute), [1] per_fate_entropy (scCS.CommitmentScoreResult attribute), [1] (scCS.scores.CommitmentScoreResult attribute), [1] plot_affinity_distributions() (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method) (scCS.PairScorer method) (scCS.pairwise.PairScorer method) plot_commitment_bar() (in module scCS) (in module scCS.plot) (scCS.single.SingleScorer method) (scCS.SingleScorer method) plot_commitment_heatmap() (in module scCS) (in module scCS.plot) (scCS.single.SingleScorer method) (scCS.SingleScorer method) plot_commitment_vector_radar() (in module scCS) (in module scCS.plot) (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method) (scCS.PairScorer method) (scCS.pairwise.PairScorer method) plot_compare_conditions_bar() (in module scCS) (in module scCS.plot) (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method) (scCS.PairScorer method) (scCS.pairwise.PairScorer method) plot_delta_cs_heatmap() (in module scCS) (in module scCS.plot) (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method) (scCS.PairScorer method) (scCS.pairwise.PairScorer method) plot_expression_trends() (in module scCS) (in module scCS.plot) plot_nn_entropy_elbow() (in module scCS) (in module scCS.plot) (scCS.single.SingleScorer method) (scCS.SingleScorer method) plot_omnibus_summary() (in module scCS) (in module scCS.plot) (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method)

plot_pairwise_cs() (in module scCS) (in module scCS.plot) (scCS.single.SingleScorer method) (scCS.SingleScorer method) plot_pairwise_delta_grid() (in module scCS) (in module scCS.plot) (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method) plot_posthoc_heatmap() (in module scCS) (in module scCS.plot) (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method) plot_rose() (in module scCS) (in module scCS.plot) (scCS.single.SingleScorer method) (scCS.SingleScorer method) plot_rose_grid() (in module scCS) (in module scCS.plot) (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method) (scCS.PairScorer method) (scCS.pairwise.PairScorer method) plot_star() (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method) (scCS.PairScorer method) (scCS.pairwise.PairScorer method) (scCS.single.SingleScorer method) (scCS.SingleScorer method) plot_star_embedding() (in module scCS) (in module scCS.plot) plot_star_grid() (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method) (scCS.PairScorer method) (scCS.pairwise.PairScorer method) plot_star_panels() (in module scCS) (in module scCS.plot) plot_subset_comparison() (in module scCS) (in module scCS.plot) (scCS.single.SingleScorer method) (scCS.SingleScorer method) plot_trajectory_shift() (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method) (scCS.PairScorer method) (scCS.pairwise.PairScorer method) population_entropy (scCS.CommitmentScoreResult attribute), [1] (scCS.scores.CommitmentScoreResult attribute), [1] PROGENITOR_COLOR (in module scCS.plot) project_velocity_star() (in module scCS.embedding)

R

refit_pseudotime() (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method) (scCS.PairScorer method) (scCS.pairwise.PairScorer method) root (scCS.bifurcation.FateMap attribute), [1] (scCS.FateMap attribute), [1] (scCS.multicomparison.MultiScorer attribute) (scCS.pairwise.PairScorer attribute)

root_cells (scCS.bifurcation.FateMap attribute), [1] (scCS.FateMap attribute), [1] root_centroid (scCS.bifurcation.FateMap attribute), [1] (scCS.FateMap attribute), [1] run_enrichment_per_fate() (in module scCS) (in module scCS.enrichment) run_velocity_pipeline() (in module scCS.embedding)

S

save() (scCS.single.SingleScorer method) (scCS.SingleScorer method) scale_metric_01() (in module scCS) (in module scCS.embedding) scCS module scCS.bifurcation module scCS.drivers module scCS.embedding module scCS.enrichment module scCS.multicomparison module scCS.pairwise module scCS.plot module scCS.scores module scCS.single module

score() (scCS.single.SingleScorer method) (scCS.SingleScorer method) score_all_conditions() (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method) (scCS.PairScorer method) (scCS.pairwise.PairScorer method) score_per_subset() (scCS.single.SingleScorer method) (scCS.SingleScorer method) scorer (scCS.multicomparison.MultiScorer property) (scCS.MultiScorer property) (scCS.PairScorer property) (scCS.pairwise.PairScorer property) sector_method (scCS.multicomparison.MultiScorer attribute) (scCS.pairwise.PairScorer attribute) sectors (scCS.CommitmentScoreResult attribute), [1] (scCS.scores.CommitmentScoreResult attribute), [1] SingleScorer (class in scCS) (class in scCS.single) summary() (scCS.bifurcation.FateMap method) (scCS.CommitmentScoreResult method) (scCS.FateMap method) (scCS.scores.CommitmentScoreResult method)

T

to_dataframe() (scCS.CommitmentScoreResult method) (scCS.scores.CommitmentScoreResult method) trajectory_shift() (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method) (scCS.PairScorer method) (scCS.pairwise.PairScorer method)

transfer_labels() (scCS.multicomparison.MultiScorer method) (scCS.MultiScorer method) (scCS.PairScorer method) (scCS.pairwise.PairScorer method) (scCS.single.SingleScorer method) (scCS.SingleScorer method)