Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X | Z A adamson_2016_pilot() (in module pertpy.data) adamson_2016_upr_epistasis() (in module pertpy.data) adamson_2016_upr_perturb_seq() (in module pertpy.data) adata (Scgen attribute) adata_manager (Scgen attribute) add() (CentroidSpace method) (DBSCANSpace method) (KMeansSpace method) (LRClassifierSpace method) (MLPClassifierSpace method) (PseudobulkSpace method) add_covariate_to_nhoods_var() (Milo method) add_nhood_expression() (Milo method) aissa_2021() (in module pertpy.data) annotate() (CellLine method) (Drug method) (Moa method) annotate_bulk_rna() (CellLine method) annotate_compounds() (Compound method) annotate_from_gdsc() (CellLine method) annotate_from_prism() (CellLine method) annotate_nhoods() (Milo method) annotate_nhoods_continuous() (Milo method) annotate_protein_expression() (CellLine method) assign_by_threshold() (GuideAssignment method) assign_mixture_model() (GuideAssignment method) assign_to_max_guide() (GuideAssignment method) assign_to_max_guide_anndata() (GuideAssignment method) assign_to_max_guide_numpy() (GuideAssignment method) assign_to_max_guide_sparse() (GuideAssignment method) attribution_scatter() (Cinemaot method) Augur (class in pertpy.tools) available_bulk_rna() (LookUp method) available_cell_lines() (LookUp method) available_compounds() (LookUp method) available_drug_annotation() (LookUp method) available_drug_response() (LookUp method) available_genes_annotation() (LookUp method) available_moa() (LookUp method) available_protein_expression() (LookUp method) average_metrics() (Augur method) B batch_removal() (Scgen method) bhattacherjee() (in module pertpy.data) bootstrap() (Distance method) build_nhood_graph() (Milo method) burczynski_crohn() (in module pertpy.data) C calculate_multifactor_PMD() (Dialogue method) causaleffect() (Cinemaot method) causaleffect_weighted() (Cinemaot method) ccc_score() (Augur method) cell_wise_metric (Distance attribute) CellLine (class in pertpy.metadata) CentroidSpace (class in pertpy.tools) chang_2021() (in module pertpy.data) Cinemaot (class in pertpy.tools) cinemaot_example() (in module pertpy.data) combosciplex() (in module pertpy.data) compare_distance() (Distance method) compare_groups() (EdgeR class method) (PermutationTest class method) (PyDESeq2 class method) (Statsmodels class method) (TTest class method) (WilcoxonTest class method) Compound (class in pertpy.metadata) compute() (CentroidSpace method) (DBSCANSpace method) (KMeansSpace method) (LRClassifierSpace method) (MLPClassifierSpace method) (PseudobulkSpace method) compute_control_diff() (CentroidSpace method) (DBSCANSpace method) (KMeansSpace method) (LRClassifierSpace method) (MLPClassifierSpace method) (PseudobulkSpace method) cond() (EdgeR method) (PyDESeq2 method) (Statsmodels method) contrast() (EdgeR method) (PyDESeq2 method) (Statsmodels method) convert_legacy_save() (Scgen class method) correlate() (CellLine method) count_nhoods() (Milo method) cox_compare() (Augur method) create_estimator() (Augur method) credible_effects() (Sccoda method) (Tasccoda method) cross_validate_subsample() (Augur method) D da_nhoods() (Milo method) data (EdgeR attribute) (PermutationTest attribute) (PyDESeq2 attribute) (Statsmodels attribute) (TTest attribute) (WilcoxonTest attribute) data_registry() (Scgen method) datlinger_2017() (in module pertpy.data) datlinger_2021() (in module pertpy.data) DBSCANSpace (class in pertpy.tools) deregister_manager() (Scgen method) device (Scgen attribute) Dialogue (class in pertpy.tools) dialogue_example() (in module pertpy.data) Distance (class in pertpy.tools) distance_example() (in module pertpy.data) DistanceTest (class in pertpy.tools) dixit_2016() (in module pertpy.data) dixit_2016_raw() (in module pertpy.data) dong_2023() (in module pertpy.data) draw_subsample() (Augur method) Drug (class in pertpy.metadata) E EdgeR (class in pertpy.tools) Enrichment (class in pertpy.tools) evaluate_clustering() (DBSCANSpace method) (KMeansSpace method) F fit() (EdgeR method) (PyDESeq2 method) (Statsmodels method) frangieh_2021() (in module pertpy.data) frangieh_2021_protein() (in module pertpy.data) frangieh_2021_raw() (in module pertpy.data) frangieh_2021_rna() (in module pertpy.data) G gasperini_2019_atscale() (in module pertpy.data) gasperini_2019_highmoi() (in module pertpy.data) gasperini_2019_lowmoi() (in module pertpy.data) gehring_2019() (in module pertpy.data) generate_pseudobulk() (Cinemaot method) get_anndata_manager() (Scgen method) get_decoded_expression() (Scgen method) get_dim() (Cinemaot method) get_effect_df() (Sccoda method) (Tasccoda method) get_extrema_MCP_genes() (Dialogue method) get_from_registry() (Scgen method) get_intercept_df() (Sccoda method) (Tasccoda method) get_latent_representation() (Scgen method) get_mlm_mcp_genes() (Dialogue method) get_node_df() (Sccoda method) (Tasccoda method) get_normalized_expression() (Scgen method) get_normalized_function_name (Scgen attribute) get_setup_arg() (Scgen method) get_state_registry() (Scgen method) get_var_names() (Scgen method) gsea() (Enrichment method) GuideAssignment (class in pertpy.preprocessing) H haber_2017_regions() (in module pertpy.data) hagai_2018() (in module pertpy.data) history (Scgen attribute) hypergeometric() (Enrichment method) I is_trained (Scgen attribute) K kang_2018() (in module pertpy.data) KMeansSpace (class in pertpy.tools) L label_transfer() (CentroidSpace method) (DBSCANSpace method) (KMeansSpace method) (LRClassifierSpace method) (MLPClassifierSpace method) (PseudobulkSpace method) layer_key (Distance attribute) lda() (Mixscape method) load() (Augur method) (Milo method) (Sccoda method) (Scgen class method) (Tasccoda method) load_registry() (Scgen static method) LookUp (class in pertpy.metadata) lookup() (CellLine method) (Compound method) (Drug method) (Moa method) LRClassifierSpace (class in pertpy.tools) M make_arviz() (Sccoda method) (Tasccoda method) make_nhoods() (Milo method) mcfarland_2020() (in module pertpy.data) metric (Distance attribute) Milo (class in pertpy.tools) Mixscape (class in pertpy.tools) mixscape() (Mixscape method) MLPClassifierSpace (class in pertpy.tools) Moa (class in pertpy.metadata) model() (Sccoda method) (Tasccoda method) multilevel_modeling() (Dialogue method) N norman_2019() (in module pertpy.data) norman_2019_raw() (in module pertpy.data) O obsm_key (Distance attribute) onesided_distances() (Distance method) P pairwise() (Distance method) papalexi_2021() (in module pertpy.data) PermutationTest (class in pertpy.tools) perturbation_signature() (Mixscape method) plot_barplot() (Mixscape method) plot_binary_classifier() (Scgen method) plot_boxplots() (Sccoda method) (Tasccoda method) plot_correlation() (CellLine method) plot_da_beeswarm() (Milo method) plot_dotplot() (Enrichment method) plot_dp_scatter() (Augur method) plot_draw_effects() (Sccoda method) (Tasccoda method) plot_draw_tree() (Sccoda method) (Tasccoda method) plot_effects_barplot() (Sccoda method) (Tasccoda method) plot_effects_umap() (Sccoda method) (Tasccoda method) plot_fold_change() (EdgeR method) (PermutationTest method) (PyDESeq2 method) (Statsmodels method) (TTest method) (WilcoxonTest method) plot_gsea() (Enrichment method) plot_heatmap() (GuideAssignment method) (Mixscape method) plot_important_features() (Augur method) plot_lda() (Mixscape method) plot_lollipop() (Augur method) plot_multicomparison_fc() (EdgeR method) (PermutationTest method) (PyDESeq2 method) (Statsmodels method) (TTest method) (WilcoxonTest method) plot_nhood() (Milo method) plot_nhood_counts_by_cond() (Milo method) plot_nhood_graph() (Milo method) plot_paired() (EdgeR method) (PermutationTest method) (PyDESeq2 method) (Statsmodels method) (TTest method) (WilcoxonTest method) plot_pairplot() (Dialogue method) plot_perturbscore() (Mixscape method) plot_reg_mean_plot() (Scgen method) plot_reg_var_plot() (Scgen method) plot_rel_abundance_dispersion_plot() (Sccoda method) (Tasccoda method) plot_scatterplot() (Augur method) plot_split_violins() (Dialogue method) plot_stacked_barplot() (Sccoda method) (Tasccoda method) plot_violin() (Mixscape method) plot_vis_matching() (Cinemaot method) plot_volcano() (EdgeR method) (PermutationTest method) (PyDESeq2 method) (Statsmodels method) (TTest method) (WilcoxonTest method) precompute_distances() (Distance method) predict() (Augur method) (Scgen method) predict_differential_prioritization() (Augur method) prepare() (Sccoda method) (Tasccoda method) PseudobulkSpace (class in pertpy.tools) PyDESeq2 (class in pertpy.tools) R register_manager() (Scgen class method) registry (Scgen attribute) replogle_2022_k562_essential() (in module pertpy.data) replogle_2022_k562_gwps() (in module pertpy.data) replogle_2022_rpe1() (in module pertpy.data) run_cross_validation() (Augur method) run_hmc() (Sccoda method) (Tasccoda method) run_id (Scgen attribute) run_name (Scgen attribute) run_nuts() (Sccoda method) (Tasccoda method) S sample() (Augur method) save() (Scgen method) sc_sim_augur() (in module pertpy.data) Sccoda (class in pertpy.tools) Scgen (class in pertpy.tools) schiebinger_2019_16day() (in module pertpy.data) schiebinger_2019_18day() (in module pertpy.data) schraivogel_2020_tap_screen_chr11() (in module pertpy.data) schraivogel_2020_tap_screen_chr8() (in module pertpy.data) sciplex3_raw() (in module pertpy.data) sciplex_gxe1() (in module pertpy.data) score() (Enrichment method) select_highly_variable() (Augur method) select_variance() (Augur method) set_fdr() (Sccoda method) (Tasccoda method) set_init_mcmc_states() (Sccoda method) (Tasccoda method) set_scorer() (Augur method) setup_anndata() (Scgen class method) shifrut_2018() (in module pertpy.data) smillie_2019() (in module pertpy.data) srivatsan_2020_sciplex2() (in module pertpy.data) srivatsan_2020_sciplex3() (in module pertpy.data) srivatsan_2020_sciplex4() (in module pertpy.data) Statsmodels (class in pertpy.tools) stephenson_2021_subsampled() (in module pertpy.data) subtract() (CentroidSpace method) (DBSCANSpace method) (KMeansSpace method) (LRClassifierSpace method) (MLPClassifierSpace method) (PseudobulkSpace method) summary() (Sccoda method) (Tasccoda method) summary_prepare() (Sccoda method) (Tasccoda method) summary_string (Scgen attribute) synergy() (Cinemaot method) T Tasccoda (class in pertpy.tools) tasccoda_example() (in module pertpy.data) test_association() (Dialogue method) test_contrasts() (EdgeR method) (PyDESeq2 method) (Statsmodels method) test_indices (Scgen attribute) test_precomputed() (DistanceTest method) test_reduced() (EdgeR method) (PyDESeq2 method) (Statsmodels method) test_xy() (DistanceTest method) tian_2019_day7neuron() (in module pertpy.data) tian_2019_ipsc() (in module pertpy.data) tian_2021_crispra() (in module pertpy.data) tian_2021_crispri() (in module pertpy.data) to_device() (Scgen method) train() (Scgen method) train_indices (Scgen attribute) transfer_fields() (Scgen method) TTest (class in pertpy.tools) U update_setup_method_args() (Scgen method) V validation_indices (Scgen attribute) variables (EdgeR attribute) (PyDESeq2 attribute) (Statsmodels attribute) view_anndata_setup() (Scgen method) view_registry() (Scgen method) view_setup_args() (Scgen static method) view_setup_method_args() (Scgen method) W weinreb_2020() (in module pertpy.data) WilcoxonTest (class in pertpy.tools) X xie_2017() (in module pertpy.data) Z zhang_2021() (in module pertpy.data) zhao_2021() (in module pertpy.data)
