Index A | B | C | D | E | F | G | I | L | M | N | O | P | Q | R | S | T | U | V | X A adata (pyroma.ROMA attribute) approx_int (pyroma.ROMA attribute) approx_size() (pyroma.ROMA method) assess_significance() (pyroma.ROMA method) B BOLD (pyroma.color attribute) C color (class in pyroma) compare_conditions() (pyroma.ROMA method) compute() (pyroma.ROMA method) compute_batch() (pyroma.ROMA method) compute_median_exp() (pyroma.ROMA method) D DARKCYAN (pyroma.color attribute) double_mean_center_matrix() (pyroma.ROMA method) E END (pyroma.color attribute) export_results() (pyroma.ROMA method) F fisher_outlier_filter() (pyroma.ROMA method) fix_pc_sign() (pyroma.ROMA method) G GeneSetResult (class in pyroma) genesets (pyroma.ROMA attribute) get_module_scores() (pyroma.ROMA method) get_raw_p_values() (pyroma.ROMA method) get_top_genes() (pyroma.ROMA method) gmt (pyroma.ROMA attribute) GREEN (pyroma.color attribute) I indexing() (pyroma.ROMA method) integrate_projection_results() (in module pyroma) L limit_outliers_per_geneset() (pyroma.ROMA method) load_active_modules_results() (pyroma.ROMA method) loocv() (pyroma.ROMA method) M med_exp_q_value (pyroma.GeneSetResult attribute) min_n_genes (pyroma.ROMA attribute) module pyroma N non_adj_med_exp_p (pyroma.GeneSetResult attribute) non_adj_p (pyroma.GeneSetResult attribute) null_distributions (pyroma.ROMA attribute) null_median_exp (pyroma.GeneSetResult attribute) null_projections (pyroma.GeneSetResult attribute) nullgenesetsize (pyroma.GeneSetResult attribute) nulll1 (pyroma.GeneSetResult attribute) O orient_pc1() (pyroma.ROMA method) outliers (pyroma.GeneSetResult attribute) P p_values_in_frame() (pyroma.ROMA method) pbmc3k() (in module pyroma) pbmc_ifnb() (in module pyroma) process_iteration() (pyroma.ROMA method) projections_1 (pyroma.GeneSetResult attribute) projections_2 (pyroma.GeneSetResult attribute) PURPLE (pyroma.color attribute) pyroma module Q q_L1_threshold (pyroma.ROMA attribute) q_Med_Exp_threshold (pyroma.ROMA attribute) q_value (pyroma.GeneSetResult attribute) R randomset_parallel() (pyroma.ROMA method) raw_X_subset (pyroma.GeneSetResult attribute) read_gmt_to_dict() (pyroma.ROMA method) results (pyroma.ROMA attribute) robustIncrementalPCA() (pyroma.ROMA method) robustPCA() (pyroma.ROMA method) robustTruncatedSVD() (pyroma.ROMA method) ROMA (class in pyroma) S save_active_modules_results() (pyroma.ROMA method) select_active_modules() (pyroma.ROMA method) select_and_sort_gene_sets() (pyroma.ROMA method) subset (pyroma.GeneSetResult attribute) subsetlist (pyroma.GeneSetResult attribute) subsetting() (pyroma.ROMA method) summary() (pyroma.ROMA method) svd (pyroma.GeneSetResult attribute) T test_l1 (pyroma.GeneSetResult attribute) test_median_exp (pyroma.GeneSetResult attribute) U use_hallmarks() (in module pyroma) use_progeny() (in module pyroma) use_reactome() (in module pyroma) V validate_results() (pyroma.ROMA method) X X (pyroma.GeneSetResult attribute)