Index

_

_PlottingNamespace (class in crispyx._namespaces) _PreprocessingNamespace (class in crispyx._namespaces)

_PseudobulkNamespace (class in crispyx._namespaces) _ToolsNamespace (class in crispyx._namespaces)

A

average_log_expression() (crispyx._namespaces._PseudobulkNamespace method)

B

beta_intercept (crispyx.glm.ControlStatisticsCache attribute)

build_design_matrix() (in module crispyx.glm)

C

cell_gene_counts (crispyx.qc.QualityControlResult attribute) cell_mask (crispyx.qc.QualityControlResult attribute) coef (crispyx.glm.NBGLMBatchResult attribute) (crispyx.glm.NBGLMResult attribute) compute_average_log_expression() (in module crispyx.pseudobulk) compute_cooks_distance_batch() (in module crispyx.glm) compute_overlap() (crispyx._namespaces._ToolsNamespace method) compute_pseudobulk_expression() (in module crispyx.pseudobulk) control_dispersion (crispyx.glm.ControlStatisticsCache attribute) control_expr_counts (crispyx.glm.ControlStatisticsCache attribute) control_label (crispyx.de.RankGenesGroupsResult attribute) control_matrix (crispyx.glm.ControlStatisticsCache attribute) control_mean_expr (crispyx.glm.ControlStatisticsCache attribute) control_n (crispyx.glm.ControlStatisticsCache attribute) control_offset (crispyx.glm.ControlStatisticsCache attribute) control_xtwx_intercept (crispyx.glm.ControlStatisticsCache attribute) control_xtwz_intercept (crispyx.glm.ControlStatisticsCache attribute) ControlStatisticsCache (class in crispyx.glm)

converged (crispyx.glm.NBGLMBatchResult attribute) (crispyx.glm.NBGLMResult attribute) convert_to_csc() (crispyx._namespaces._PreprocessingNamespace method) convert_to_csr() (crispyx._namespaces._PreprocessingNamespace method) crispyx.de module crispyx.dimred module crispyx.glm module crispyx.plotting module crispyx.profiling module crispyx.pseudobulk module crispyx.qc module

D

deviance (crispyx.glm.NBGLMBatchResult attribute) (crispyx.glm.NBGLMResult attribute) DifferentialExpressionResult (class in crispyx.de)

dispersion (crispyx.glm.NBGLMBatchResult attribute) (crispyx.glm.NBGLMResult attribute) dispersion_scope (crispyx.glm.ControlStatisticsCache attribute)

E

effect_size (crispyx.de.DifferentialExpressionResult attribute) (crispyx.de.RankGenesGroupsResult attribute) estimate_covariate_effects_streaming() (in module crispyx.glm)

estimate_dispersion_cox_reid() (crispyx.glm.NBGLMFitter method) estimate_dispersion_map() (in module crispyx.glm) estimate_global_dispersion_streaming() (in module crispyx.glm)

F

filter_cells() (crispyx._namespaces._PreprocessingNamespace method) filter_cells_by_gene_count() (in module crispyx.qc) filter_genes() (crispyx._namespaces._PreprocessingNamespace method) filter_genes_by_cell_count() (in module crispyx.qc) filter_outliers_cooks() (in module crispyx.glm) filter_perturbations() (crispyx._namespaces._PreprocessingNamespace method) filter_perturbations_by_cell_count() (in module crispyx.qc) filtered (crispyx.qc.QualityControlResult attribute) filtered_path (crispyx.qc.QualityControlResult property) fit_batch() (crispyx.glm.NBGLMBatchFitter method) fit_batch_with_control_cache() (crispyx.glm.NBGLMBatchFitter method)

fit_batch_with_covariate_offset() (crispyx.glm.NBGLMBatchFitter method) fit_batch_with_frozen_control() (crispyx.glm.NBGLMBatchFitter method) fit_batch_with_joint_offsets() (crispyx.glm.NBGLMBatchFitter method) fit_dispersion_trend() (in module crispyx.glm) fit_gene() (crispyx.glm.NBGLMFitter method) fit_matrix() (crispyx.glm.NBGLMFitter method) frozen_control_mu_sum (crispyx.glm.ControlStatisticsCache attribute) frozen_control_resid_sq_sum (crispyx.glm.ControlStatisticsCache attribute) frozen_control_W_sum (crispyx.glm.ControlStatisticsCache attribute) frozen_control_Wz_sum (crispyx.glm.ControlStatisticsCache attribute) frozen_control_Y_sum (crispyx.glm.ControlStatisticsCache attribute)

G

gene_cell_counts (crispyx.qc.QualityControlResult attribute) gene_mask (crispyx.qc.QualityControlResult attribute) genes (crispyx.de.DifferentialExpressionResult attribute) (crispyx.de.RankGenesGroupsResult attribute) get_report() (crispyx.profiling.Profiler method) get_stats() (crispyx.profiling.Profiler method)

get_total_time() (crispyx.profiling.Profiler method) global_disp_prior_var (crispyx.glm.ControlStatisticsCache attribute) global_dispersion (crispyx.glm.ControlStatisticsCache attribute) global_dispersion_trend (crispyx.glm.ControlStatisticsCache attribute) global_size_factors (crispyx.glm.ControlStatisticsCache attribute) groupby (crispyx.de.RankGenesGroupsResult attribute) groups (crispyx.de.RankGenesGroupsResult attribute)

I

items() (crispyx.de.RankGenesGroupsResult method)

L

logfoldchanges (crispyx.de.RankGenesGroupsResult attribute)

M

ma() (crispyx._namespaces._PlottingNamespace method) materialize_rank_genes_groups() (crispyx._namespaces._PlottingNamespace method) (in module crispyx.plotting) max_cooks (crispyx.glm.NBGLMResult attribute) MemoryProfiler (class in crispyx.profiling) method (crispyx.de.DifferentialExpressionResult attribute) (crispyx.de.RankGenesGroupsResult attribute)

module crispyx.de crispyx.dimred crispyx.glm crispyx.plotting crispyx.profiling crispyx.pseudobulk crispyx.qc

N

n_iter (crispyx.glm.NBGLMBatchResult attribute) (crispyx.glm.NBGLMResult attribute) nb_glm_test() (in module crispyx.de) NBGLMBatchFitter (class in crispyx.glm) NBGLMBatchResult (class in crispyx.glm)

NBGLMFitter (class in crispyx.glm) NBGLMResult (class in crispyx.glm) neighbors() (crispyx._namespaces._PreprocessingNamespace method) (in module crispyx.dimred) normalize_total_log1p() (crispyx._namespaces._PreprocessingNamespace method)

O

order (crispyx.de.RankGenesGroupsResult attribute)

overlap_heatmap() (crispyx._namespaces._PlottingNamespace method)

P

pca() (crispyx._namespaces._PlottingNamespace method) (crispyx._namespaces._PreprocessingNamespace method) (in module crispyx.dimred) pca_loadings() (crispyx._namespaces._PlottingNamespace method) pca_variance_ratio() (crispyx._namespaces._PlottingNamespace method) perturbation (crispyx.de.DifferentialExpressionResult attribute) perturbation_keep (crispyx.qc.QualityControlResult attribute) plot_ma() (in module crispyx.plotting) plot_memory() (crispyx.profiling.Profiler method) plot_overlap_heatmap() (in module crispyx.plotting) plot_pca() (in module crispyx.plotting) plot_pca_loadings() (in module crispyx.plotting) plot_pca_variance_ratio() (in module crispyx.plotting) plot_qc_perturbation_counts() (in module crispyx.plotting) plot_qc_summary() (in module crispyx.plotting) plot_timeline() (crispyx.profiling.Profiler method)

plot_top_genes_bar() (in module crispyx.plotting) plot_umap() (in module crispyx.plotting) plot_volcano() (in module crispyx.plotting) precompute_control_statistics() (in module crispyx.glm) precompute_control_statistics_streaming() (in module crispyx.glm) precompute_global_dispersion() (in module crispyx.glm) precompute_global_dispersion_from_path() (in module crispyx.glm) Profiler (class in crispyx.profiling) pseudobulk() (crispyx._namespaces._PseudobulkNamespace method) pts (crispyx.de.RankGenesGroupsResult attribute) pts_rest (crispyx.de.RankGenesGroupsResult attribute) (crispyx.glm.ControlStatisticsCache attribute) pvalue (crispyx.de.DifferentialExpressionResult attribute) pvalue_adj (crispyx.de.DifferentialExpressionResult attribute) pvalue_correction (crispyx.de.RankGenesGroupsResult attribute) pvalues (crispyx.de.RankGenesGroupsResult attribute) pvalues_adj (crispyx.de.RankGenesGroupsResult attribute)

Q

qc_perturbation_counts() (crispyx._namespaces._PlottingNamespace method) qc_summary() (crispyx._namespaces._PlottingNamespace method) (crispyx._namespaces._PreprocessingNamespace method)

quality_control_summary() (in module crispyx.qc) QualityControlResult (class in crispyx.qc)

R

rank_genes_groups() (crispyx._namespaces._PlottingNamespace method) (crispyx._namespaces._ToolsNamespace method) (in module crispyx.plotting) rank_genes_groups_df() (crispyx._namespaces._PlottingNamespace method) (in module crispyx.plotting)

RankGenesGroupsResult (class in crispyx.de) reset_peak() (crispyx.profiling.Profiler method) result (crispyx.de.DifferentialExpressionResult attribute) (crispyx.de.RankGenesGroupsResult attribute) result_path (crispyx.de.DifferentialExpressionResult property) (crispyx.de.RankGenesGroupsResult property)

S

se (crispyx.glm.NBGLMBatchResult attribute) (crispyx.glm.NBGLMResult attribute) shrink_dispersions() (in module crispyx.glm) shrink_lfc() (crispyx._namespaces._ToolsNamespace method) (in module crispyx.de) shrink_lfc_apeglm() (in module crispyx.glm) shrink_lfc_apeglm_from_stats() (in module crispyx.glm)

snapshot() (crispyx.profiling.Profiler method) start() (crispyx.profiling.Profiler method) start_sampling() (crispyx.profiling.Profiler method) statistic (crispyx.de.DifferentialExpressionResult attribute) statistics (crispyx.de.RankGenesGroupsResult attribute) stop() (crispyx.profiling.Profiler method) stop_sampling() (crispyx.profiling.Profiler method)

T

t_test() (in module crispyx.de) tie_correct (crispyx.de.RankGenesGroupsResult attribute) TimingProfiler (class in crispyx.profiling)

to_full_order_dict() (crispyx.de.RankGenesGroupsResult method) to_rank_genes_groups_dict() (crispyx.de.RankGenesGroupsResult method) top_genes_bar() (crispyx._namespaces._PlottingNamespace method)

U

u_statistics (crispyx.de.RankGenesGroupsResult attribute) umap() (crispyx._namespaces._PlottingNamespace method) (crispyx._namespaces._ToolsNamespace method) (in module crispyx.dimred)

use_frozen_control (crispyx.glm.ControlStatisticsCache attribute)

V

volcano() (crispyx._namespaces._PlottingNamespace method)

W

wilcoxon_test() (in module crispyx.de)