Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | 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 (pertpy.tools.SCGEN attribute) adata_manager (pertpy.tools.SCGEN attribute) add() (pertpy.tools.CentroidSpace method) (pertpy.tools.DBSCANSpace method) (pertpy.tools.KMeansSpace method) (pertpy.tools.LRClassifierSpace method) (pertpy.tools.MLPClassifierSpace method) (pertpy.tools.PseudobulkSpace method) add_covariate_to_nhoods_var() (pertpy.tools.Milo method) add_nhood_expression() (pertpy.tools.Milo method) aissa_2021() (in module pertpy.data) annotate() (pertpy.metadata.CellLine method) (pertpy.metadata.Drug method) (pertpy.metadata.Moa method) annotate_bulk_rna() (pertpy.metadata.CellLine method) annotate_compounds() (pertpy.metadata.Compound method) annotate_from_gdsc() (pertpy.metadata.CellLine method) annotate_nhoods() (pertpy.tools.Milo method) annotate_nhoods_continuous() (pertpy.tools.Milo method) annotate_protein_expression() (pertpy.metadata.CellLine method) assign_by_threshold() (pertpy.preprocessing.GuideAssignment method) assign_to_max_guide() (pertpy.preprocessing.GuideAssignment method) attribution_scatter() (pertpy.tools.Cinemaot method) Augur (class in pertpy.tools) average_metrics() (pertpy.tools.Augur method) B batch_removal() (pertpy.tools.SCGEN method) bhattacherjee() (in module pertpy.data) build_nhood_graph() (pertpy.tools.Milo method) burczynski_crohn() (in module pertpy.data) C calculate_cohens_d() (pertpy.tools.DifferentialGeneExpression method) calculate_correlation() (pertpy.tools.DifferentialGeneExpression method) calculate_jaccard_index() (pertpy.tools.DifferentialGeneExpression method) calculate_multifactor_PMD() (pertpy.tools.Dialogue method) causaleffect() (pertpy.tools.Cinemaot method) causaleffect_weighted() (pertpy.tools.Cinemaot method) ccc_score() (pertpy.tools.Augur method) cell_wise_metric (pertpy.tools.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) Compound (class in pertpy.metadata) compute() (pertpy.tools.CentroidSpace method) (pertpy.tools.DBSCANSpace method) (pertpy.tools.KMeansSpace method) (pertpy.tools.LRClassifierSpace method) (pertpy.tools.MLPClassifierSpace method) (pertpy.tools.PseudobulkSpace method) compute_control_diff() (pertpy.tools.CentroidSpace method) (pertpy.tools.DBSCANSpace method) (pertpy.tools.KMeansSpace method) (pertpy.tools.LRClassifierSpace method) (pertpy.tools.MLPClassifierSpace method) (pertpy.tools.PseudobulkSpace method) convert_legacy_save() (pertpy.tools.SCGEN class method) correlate() (pertpy.metadata.CellLine method) count_nhoods() (pertpy.tools.Milo method) cox_compare() (pertpy.tools.Augur method) create_estimator() (pertpy.tools.Augur method) credible_effects() (pertpy.tools.Sccoda method) (pertpy.tools.Tasccoda method) cross_validate_subsample() (pertpy.tools.Augur method) D da_nhoods() (pertpy.tools.Milo method) datlinger_2017() (in module pertpy.data) datlinger_2021() (in module pertpy.data) DBSCANSpace (class in pertpy.tools) de_analysis() (pertpy.tools.DifferentialGeneExpression method) de_res_to_anndata() (pertpy.tools.DifferentialGeneExpression method) deregister_manager() (pertpy.tools.SCGEN method) device (pertpy.tools.SCGEN attribute) Dialogue (class in pertpy.tools) dialogue_example() (in module pertpy.data) DifferentialGeneExpression (class in pertpy.tools) Distance (class in pertpy.tools) DistanceTest (class in pertpy.tools) dixit_2016() (in module pertpy.data) dixit_2016_raw() (in module pertpy.data) draw_subsample() (pertpy.tools.Augur method) Drug (class in pertpy.metadata) E Enrichment (class in pertpy.tools) evaluate_clustering() (pertpy.tools.DBSCANSpace method) (pertpy.tools.KMeansSpace method) F filter_by_expr() (pertpy.tools.DifferentialGeneExpression method) filter_by_prop() (pertpy.tools.DifferentialGeneExpression 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() (pertpy.tools.Cinemaot method) get_anndata_manager() (pertpy.tools.SCGEN method) get_decoded_expression() (pertpy.tools.SCGEN method) get_dim() (pertpy.tools.Cinemaot method) get_effect_df() (pertpy.tools.Sccoda method) (pertpy.tools.Tasccoda method) get_embeddings() (pertpy.tools.MLPClassifierSpace method) get_extrema_MCP_genes() (pertpy.tools.Dialogue method) get_from_registry() (pertpy.tools.SCGEN method) get_intercept_df() (pertpy.tools.Sccoda method) (pertpy.tools.Tasccoda method) get_latent_representation() (pertpy.tools.SCGEN method) get_mlm_mcp_genes() (pertpy.tools.Dialogue method) get_node_df() (pertpy.tools.Sccoda method) (pertpy.tools.Tasccoda method) get_pseudobulk() (pertpy.tools.DifferentialGeneExpression method) get_weightidx() (pertpy.tools.Cinemaot method) gsea() (pertpy.tools.Enrichment method) GuideAssignment (class in pertpy.preprocessing) H haber_2017_regions() (in module pertpy.data) history (pertpy.tools.SCGEN attribute) hypergeometric() (pertpy.tools.Enrichment method) I is_trained (pertpy.tools.SCGEN attribute) K kang_2018() (in module pertpy.data) KMeansSpace (class in pertpy.tools) L label_transfer() (pertpy.tools.CentroidSpace method) (pertpy.tools.DBSCANSpace method) (pertpy.tools.KMeansSpace method) (pertpy.tools.LRClassifierSpace method) (pertpy.tools.MLPClassifierSpace method) (pertpy.tools.PseudobulkSpace method) layer_key (pertpy.tools.Distance attribute) lda() (pertpy.tools.Mixscape method) load() (pertpy.tools.Augur method) (pertpy.tools.Milo method) (pertpy.tools.MLPClassifierSpace method) (pertpy.tools.Sccoda method) (pertpy.tools.SCGEN class method) (pertpy.tools.Tasccoda method) load_registry() (pertpy.tools.SCGEN static method) lookup() (pertpy.metadata.CellLine method) (pertpy.metadata.Compound method) (pertpy.metadata.Drug method) (pertpy.metadata.Moa method) LRClassifierSpace (class in pertpy.tools) M make_arviz() (pertpy.tools.Sccoda method) (pertpy.tools.Tasccoda method) make_nhoods() (pertpy.tools.Milo method) mcfarland_2020() (in module pertpy.data) metric (pertpy.tools.Distance attribute) Milo (class in pertpy.tools) Mixscape (class in pertpy.tools) mixscape() (pertpy.tools.Mixscape method) MLPClassifierSpace (class in pertpy.tools) Moa (class in pertpy.metadata) model() (pertpy.tools.Sccoda method) (pertpy.tools.Tasccoda method) multilevel_modeling() (pertpy.tools.Dialogue method) N norman_2019() (in module pertpy.data) norman_2019_raw() (in module pertpy.data) O obsm_key (pertpy.tools.Distance attribute) onesided_distances() (pertpy.tools.Distance method) P pairwise() (pertpy.tools.Distance method) papalexi_2021() (in module pertpy.data) perturbation_signature() (pertpy.tools.Mixscape method) plot_barplot() (pertpy.tools.Mixscape method) plot_binary_classifier() (pertpy.tools.SCGEN method) plot_boxplots() (pertpy.tools.Sccoda method) (pertpy.tools.Tasccoda method) plot_correlation() (pertpy.metadata.CellLine method) plot_da_beeswarm() (pertpy.tools.Milo method) plot_dotplot() (pertpy.tools.Enrichment method) plot_dp_scatter() (pertpy.tools.Augur method) plot_draw_effects() (pertpy.tools.Sccoda method) (pertpy.tools.Tasccoda method) plot_draw_tree() (pertpy.tools.Sccoda method) (pertpy.tools.Tasccoda method) plot_effects_barplot() (pertpy.tools.Sccoda method) (pertpy.tools.Tasccoda method) plot_effects_umap() (pertpy.tools.Sccoda method) (pertpy.tools.Tasccoda method) plot_gsea() (pertpy.tools.Enrichment method) plot_heatmap() (pertpy.preprocessing.GuideAssignment method) (pertpy.tools.Mixscape method) plot_important_features() (pertpy.tools.Augur method) plot_lda() (pertpy.tools.Mixscape method) plot_lollipop() (pertpy.tools.Augur method) plot_nhood() (pertpy.tools.Milo method) plot_nhood_counts_by_cond() (pertpy.tools.Milo method) plot_nhood_graph() (pertpy.tools.Milo method) plot_pairplot() (pertpy.tools.Dialogue method) plot_perturbscore() (pertpy.tools.Mixscape method) plot_reg_mean_plot() (pertpy.tools.SCGEN method) plot_reg_var_plot() (pertpy.tools.SCGEN method) plot_rel_abundance_dispersion_plot() (pertpy.tools.Sccoda method) (pertpy.tools.Tasccoda method) plot_scatterplot() (pertpy.tools.Augur method) plot_split_violins() (pertpy.tools.Dialogue method) plot_stacked_barplot() (pertpy.tools.Sccoda method) (pertpy.tools.Tasccoda method) plot_violin() (pertpy.tools.Mixscape method) plot_vis_matching() (pertpy.tools.Cinemaot method) precompute_distances() (pertpy.tools.Distance method) predict() (pertpy.tools.Augur method) (pertpy.tools.SCGEN method) predict_differential_prioritization() (pertpy.tools.Augur method) prepare() (pertpy.tools.Sccoda method) (pertpy.tools.Tasccoda method) PseudobulkSpace (class in pertpy.tools) R register_manager() (pertpy.tools.SCGEN class method) 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() (pertpy.tools.Augur method) run_hmc() (pertpy.tools.Sccoda method) (pertpy.tools.Tasccoda method) run_nuts() (pertpy.tools.Sccoda method) (pertpy.tools.Tasccoda method) S sample() (pertpy.tools.Augur method) save() (pertpy.tools.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) score() (pertpy.tools.Enrichment method) select_highly_variable() (pertpy.tools.Augur method) select_variance() (pertpy.tools.Augur method) set_fdr() (pertpy.tools.Sccoda method) (pertpy.tools.Tasccoda method) set_init_mcmc_states() (pertpy.tools.Sccoda method) (pertpy.tools.Tasccoda method) set_scorer() (pertpy.tools.Augur method) setup_anndata() (pertpy.tools.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) stephenson_2021_subsampled() (in module pertpy.data) subtract() (pertpy.tools.CentroidSpace method) (pertpy.tools.DBSCANSpace method) (pertpy.tools.KMeansSpace method) (pertpy.tools.LRClassifierSpace method) (pertpy.tools.MLPClassifierSpace method) (pertpy.tools.PseudobulkSpace method) summary() (pertpy.tools.Sccoda method) (pertpy.tools.Tasccoda method) summary_prepare() (pertpy.tools.Sccoda method) (pertpy.tools.Tasccoda method) summary_string (pertpy.tools.SCGEN attribute) synergy() (pertpy.tools.Cinemaot method) T Tasccoda (class in pertpy.tools) test_association() (pertpy.tools.Dialogue method) test_indices (pertpy.tools.SCGEN attribute) test_precomputed() (pertpy.tools.DistanceTest method) test_xy() (pertpy.tools.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() (pertpy.tools.SCGEN method) train() (pertpy.tools.MLPClassifierSpace method) (pertpy.tools.SCGEN method) train_indices (pertpy.tools.SCGEN attribute) V validation_indices (pertpy.tools.SCGEN attribute) view_anndata_setup() (pertpy.tools.SCGEN method) view_setup_args() (pertpy.tools.SCGEN static method) W weinreb_2020() (in module pertpy.data) X xie_2017() (in module pertpy.data) Z zhao_2021() (in module pertpy.data)