Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | W A abundances (ecotyper.recovery_steps.StateRecovery attribute) align_rows() (in module ecotyper.recovery_steps) annotation (ecotyper.recovery_steps.StateRecovery attribute) annotation_from_anndata() (in module ecotyper.io) apply_mean_rows() (in module ecotyper.rcompat.stats) assign_samples() (in module ecotyper.discovery_steps) assign_samples_scrna() (in module ecotyper.discovery_scrna) assignment (ecotyper.recovery_steps.EcotypeRecovery attribute) (ecotyper.recovery_steps.StateRecovery attribute) assignment_p_vals (ecotyper.recovery_steps.EcotypeRecovery attribute) average_fc_marker_genes() (in module ecotyper.recovery_steps) B binary (ecotyper.discovery_steps.Ecotypes attribute) builtin_model_path() (in module ecotyper.builtin) C cache_dir() (in module ecotyper.builtin) cell_type (ecotyper.discovery_scrna.CrossCor attribute) (ecotyper.discovery_scrna.ScFeatures attribute) (ecotyper.discovery_steps.Features attribute) (ecotyper.discovery_steps.InitialStates attribute) (ecotyper.discovery_steps.States attribute) (ecotyper.model.CellTypeModel attribute) (ecotyper.recovery_steps.StateRecovery attribute) cell_type_order (ecotyper.model.EcoTyperModel property) cell_type_specific_genes() (in module ecotyper.discovery_scrna) cell_types (ecotyper.model.EcoTyperModel attribute) CellTypeModel (class in ecotyper.model) col_apply_mean() (in module ecotyper.rcompat.stats) col_means() (in module ecotyper.rcompat.stats) col_normalize() (in module ecotyper.rcompat.stats) combined_state_abundances (ecotyper.recovery_steps.EcotypeRecovery attribute) COMMIT (in module ecotyper.builtin) compare_files() (in module ecotyper.validate) compare_trees() (in module ecotyper.validate) connectivity() (ecotyper.nmf.NMFFit method) consensus (ecotyper.nmf.NMFMerged attribute) converged (ecotyper.nmf.NMFFit attribute) cophcor() (in module ecotyper.nmf) cophenetic() (in module ecotyper.rcompat.cluster) copy() (ecotyper.rcompat.rng.RRandom method) cor (ecotyper.discovery_scrna.CrossCor attribute) cor_matrix() (in module ecotyper.rcompat.stats) cor_vectors() (in module ecotyper.rcompat.stats) cross_correlation() (in module ecotyper.discovery_scrna) CrossCor (class in ecotyper.discovery_scrna) cutree() (in module ecotyper.rcompat.cluster) D de_subsample() (in module ecotyper.discovery_scrna) deviance (ecotyper.nmf.NMFFit attribute) discover_ecotypes() (in module ecotyper.discovery_steps) discover_ecotypes_scrna() (in module ecotyper.discovery_scrna) discover_files() (in module ecotyper.workflows) discover_from_profiles() (in module ecotyper.workflows) discover_scrna() (in module ecotyper.workflows) discover_scrna_frame() (in module ecotyper.workflows) discovery() (in module ecotyper.api) discovery_result (ecotyper.model.EcoTyperModel attribute) DiscoveryResult (class in ecotyper.workflows) dispersion() (in module ecotyper.nmf) dist_euclidean_rows() (in module ecotyper.rcompat.cluster) do_cv() (in module ecotyper.discovery_scrna) do_de() (in module ecotyper.discovery_scrna) E ecotype_abundance (ecotyper.recovery_steps.EcotypeRecovery attribute) ecotype_abundances_long() (in module ecotyper.workflows) ecotype_levels() (in module ecotyper.model) ecotype_names (ecotyper.model.EcoTyperModel property) ecotyper.api module ecotyper.builtin module ecotyper.cli module ecotyper.discovery_scrna module ecotyper.discovery_steps module ecotyper.io module ecotyper.model module ecotyper.nmf module ecotyper.rcompat module ecotyper.rcompat.cluster module ecotyper.rcompat.collate module ecotyper.rcompat.fma module ecotyper.rcompat.frame module ecotyper.rcompat.io module ecotyper.rcompat.parse module ecotyper.rcompat.rng module ecotyper.rcompat.stats module ecotyper.recovery_steps module ecotyper.rlayout module ecotyper.validate module ecotyper.workflows module EcotypeRecovery (class in ecotyper.recovery_steps) EcoTyperModel (class in ecotyper.model) Ecotypes (class in ecotyper.discovery_steps) ecotypes (ecotyper.discovery_steps.Ecotypes attribute) (ecotyper.model.EcoTyperModel attribute) (ecotyper.recovery_steps.EcotypeRecovery attribute) expression (ecotyper.recovery_steps.StateRecovery attribute) extra (ecotyper.recovery_steps.StateRecovery attribute) extract_features() (in module ecotyper.discovery_steps) extract_features_scrna() (in module ecotyper.discovery_scrna) F factor_codes() (in module ecotyper.nmf) factor_levels() (in module ecotyper.rcompat.frame) fast_cor() (in module ecotyper.discovery_scrna) (in module ecotyper.rcompat.stats) Features (class in ecotyper.discovery_steps) filtered (ecotyper.discovery_scrna.SpecificGenes attribute) first_filter() (in module ecotyper.discovery_steps) first_filter_data (ecotyper.discovery_steps.States attribute) fit (ecotyper.nmf.NMFMerged attribute) fitted() (in module ecotyper.nmf) fma() (in module ecotyper.rcompat.fma) format_real() (in module ecotyper.rcompat.io) format_rows() (in module ecotyper.rcompat.io) fractions (ecotyper.model.EcoTyperModel attribute) from_anndata() (in module ecotyper.io) from_discovery() (ecotyper.model.EcoTyperModel class method) full_fcs (ecotyper.discovery_scrna.ScFeatures attribute) full_scaled (ecotyper.discovery_scrna.ScFeatures attribute) (ecotyper.discovery_steps.Features attribute) G gene_info (ecotyper.discovery_steps.States attribute) (ecotyper.model.CellTypeModel attribute) get_collation() (in module ecotyper.rcompat.collate) get_fc_for_clusters() (in module ecotyper.discovery_steps) get_variable_genes() (in module ecotyper.discovery_steps) H H (ecotyper.discovery_steps.InitialStates attribute) (ecotyper.nmf.NMFFit attribute) (ecotyper.recovery_steps.StateRecovery attribute) HClust (class in ecotyper.rcompat.cluster) hclust() (in module ecotyper.rcompat.cluster) heatmap_data (ecotyper.discovery_steps.States attribute) (ecotyper.recovery_steps.StateRecovery attribute) heatmap_genes (ecotyper.model.CellTypeModel attribute) heatmap_top_ann (ecotyper.discovery_steps.States attribute) (ecotyper.recovery_steps.StateRecovery attribute) height (ecotyper.rcompat.cluster.HClust attribute) I infer_data_type() (in module ecotyper.api) initial_abundances (ecotyper.discovery_steps.InitialStates attribute) (ecotyper.recovery_steps.StateRecovery attribute) initial_assignment (ecotyper.discovery_steps.InitialStates attribute) (ecotyper.recovery_steps.EcotypeRecovery attribute) (ecotyper.recovery_steps.StateRecovery attribute) initial_ecotypes (ecotyper.discovery_steps.Ecotypes attribute) initial_gene_info (ecotyper.discovery_steps.InitialStates attribute) (ecotyper.model.CellTypeModel attribute) initial_states() (in module ecotyper.discovery_steps) InitialStates (class in ecotyper.discovery_steps) J jaccard (ecotyper.discovery_steps.Ecotypes attribute) K kl_divergence() (in module ecotyper.nmf) L labels (ecotyper.rcompat.cluster.HClust attribute) load() (ecotyper.model.EcoTyperModel class method) load_cell_type() (in module ecotyper.model) log (ecotyper.discovery_steps.States attribute) log2p1() (in module ecotyper.rcompat.stats) log_data (ecotyper.discovery_scrna.CrossCor attribute) (ecotyper.discovery_steps.Features attribute) log_full (ecotyper.discovery_scrna.ScFeatures attribute) log_top (ecotyper.discovery_scrna.ScFeatures attribute) log_transform() (in module ecotyper.discovery_steps) M main() (in module ecotyper.cli) make_names() (in module ecotyper.rcompat.frame) make_unique() (in module ecotyper.rcompat.frame) mapping (ecotyper.discovery_steps.States attribute) (ecotyper.model.CellTypeModel attribute) mapping_all_states (ecotyper.discovery_steps.Ecotypes attribute) merge (ecotyper.rcompat.cluster.HClust attribute) merge_runs() (in module ecotyper.nmf) method (ecotyper.rcompat.cluster.HClust attribute) model_ecotypes_table() (in module ecotyper.model) MODEL_FILES (in module ecotyper.builtin) module ecotyper.api ecotyper.builtin ecotyper.cli ecotyper.discovery_scrna ecotyper.discovery_steps ecotyper.io ecotyper.model ecotyper.nmf ecotyper.rcompat ecotyper.rcompat.cluster ecotyper.rcompat.collate ecotyper.rcompat.fma ecotyper.rcompat.frame ecotyper.rcompat.io ecotyper.rcompat.parse ecotyper.rcompat.rng ecotyper.rcompat.stats ecotyper.recovery_steps ecotyper.rlayout ecotyper.validate ecotyper.workflows N n_clusters (ecotyper.discovery_steps.Ecotypes attribute) n_states (ecotyper.model.CellTypeModel attribute) (ecotyper.model.EcoTyperModel property) name (ecotyper.model.EcoTyperModel attribute) niter (ecotyper.nmf.NMFFit attribute) (ecotyper.recovery_steps.StateRecovery attribute) nmf_brunet() (in module ecotyper.nmf) nmf_cd() (in module ecotyper.nmf) nmf_input() (in module ecotyper.discovery_steps) nmf_predict() (in module ecotyper.nmf) NMFFit (class in ecotyper.nmf) NMFMerged (class in ecotyper.nmf) nrun (ecotyper.nmf.NMFMerged attribute) O order (ecotyper.rcompat.cluster.HClust attribute) P p_adjust_bh() (in module ecotyper.rcompat.stats) path (ecotyper.model.CellTypeModel attribute) (ecotyper.model.EcoTyperModel attribute) permute_rows() (ecotyper.rcompat.rng.RRandom method) phyper_upper() (in module ecotyper.rcompat.stats) pnorm() (in module ecotyper.rcompat.stats) posneg() (in module ecotyper.nmf) predict() (ecotyper.nmf.NMFFit method) predict_columns() (in module ecotyper.nmf) prepare_bulk_expression() (in module ecotyper.recovery_steps) pt() (in module ecotyper.rcompat.stats) Q quantile7() (in module ecotyper.rcompat.stats) R r_mad() (in module ecotyper.rcompat.stats) r_match() (in module ecotyper.rcompat.frame) r_mean() (in module ecotyper.rcompat.stats) r_median() (in module ecotyper.rcompat.stats) r_merge() (in module ecotyper.rcompat.frame) r_order() (in module ecotyper.rcompat.frame) r_parse() (in module ecotyper.rcompat.parse) r_sd() (in module ecotyper.rcompat.stats) r_sum() (in module ecotyper.rcompat.stats) r_var() (in module ecotyper.rcompat.stats) random_seed (ecotyper.rcompat.rng.RRandom property) rank (ecotyper.discovery_steps.InitialStates attribute) (ecotyper.discovery_steps.States attribute) rank_average() (in module ecotyper.rcompat.stats) rank_data (ecotyper.model.EcoTyperModel attribute) rank_metrics() (in module ecotyper.discovery_steps) raw (ecotyper.discovery_scrna.SpecificGenes attribute) read_annotation() (in module ecotyper.io) read_bulk_matrix() (in module ecotyper.io) read_clinical() (in module ecotyper.recovery_steps) read_delim() (in module ecotyper.rcompat.io) read_expression() (in module ecotyper.rcompat.io) read_fractions() (in module ecotyper.io) read_matrix() (in module ecotyper.rcompat.io) read_numeric_table() (in module ecotyper.rcompat.parse) read_profiles() (in module ecotyper.workflows) read_scrna_matrix() (in module ecotyper.io) read_visium() (in module ecotyper.workflows) read_W() (in module ecotyper.model) recover_bulk() (in module ecotyper.workflows) recover_bulk_files() (in module ecotyper.workflows) recover_bulk_frame() (in module ecotyper.workflows) recover_ecotypes() (in module ecotyper.recovery_steps) recover_ecotypes_scrna() (in module ecotyper.recovery_steps) recover_scrna() (in module ecotyper.workflows) recover_scrna_files() (in module ecotyper.workflows) recover_scrna_frame() (in module ecotyper.workflows) recover_states() (in module ecotyper.recovery_steps) recover_visium_files() (in module ecotyper.workflows) recover_visium_frame() (in module ecotyper.workflows) recovery() (in module ecotyper.api) reorder_dendrogram_order() (in module ecotyper.nmf) rnmf() (in module ecotyper.nmf) row_means() (in module ecotyper.rcompat.stats) row_ranks() (in module ecotyper.rcompat.stats) row_var() (in module ecotyper.rcompat.stats) row_wilcoxon_from_ranks() (in module ecotyper.rcompat.stats) row_wilcoxon_twosample() (in module ecotyper.rcompat.stats) RRandom (class in ecotyper.rcompat.rng) run_brunet() (in module ecotyper.nmf) run_nmf() (in module ecotyper.discovery_steps) runif() (ecotyper.rcompat.rng.RRandom method) runs_used (ecotyper.nmf.NMFMerged attribute) S sample() (ecotyper.rcompat.rng.RRandom method) sample_int() (ecotyper.rcompat.rng.RRandom method) save() (ecotyper.model.EcoTyperModel method) scale_data() (in module ecotyper.discovery_steps) scale_rows() (in module ecotyper.rcompat.stats) scale_vec() (in module ecotyper.rcompat.stats) scaled (ecotyper.recovery_steps.StateRecovery attribute) scaled_filt (ecotyper.discovery_scrna.CrossCor attribute) scaled_full (ecotyper.discovery_scrna.CrossCor attribute) ScFeatures (class in ecotyper.discovery_scrna) seed (ecotyper.nmf.NMFFit attribute) select_ranks() (in module ecotyper.discovery_steps) set_collation() (in module ecotyper.rcompat.collate) set_seed() (ecotyper.rcompat.rng.RRandom method) silhouette (ecotyper.discovery_steps.Ecotypes attribute) silhouette_avg_width() (in module ecotyper.rcompat.cluster) silhouette_avg_width_dist() (in module ecotyper.rcompat.cluster) silhouette_initial (ecotyper.discovery_steps.Ecotypes attribute) silhouette_widths() (in module ecotyper.rcompat.cluster) silhouettes() (in module ecotyper.nmf) sort_key() (in module ecotyper.rcompat.collate) sorted_strings() (in module ecotyper.rcompat.collate) spatial_ecotypes() (in module ecotyper.recovery_steps) spatial_states() (in module ecotyper.recovery_steps) SpecificGenes (class in ecotyper.discovery_scrna) state_abundances (ecotyper.discovery_steps.States attribute) state_assignment (ecotyper.discovery_steps.States attribute) StateRecovery (class in ecotyper.recovery_steps) States (class in ecotyper.discovery_steps) T text_roundtrip() (in module ecotyper.rcompat.parse) to_anndata() (in module ecotyper.io) top_fcs (ecotyper.discovery_scrna.ScFeatures attribute) top_log2 (ecotyper.discovery_steps.Features attribute) top_scaled (ecotyper.discovery_scrna.ScFeatures attribute) (ecotyper.discovery_steps.Features attribute) TTestError U unif_rand() (ecotyper.rcompat.rng.RRandom method) W W (ecotyper.discovery_steps.InitialStates attribute) (ecotyper.model.CellTypeModel attribute) (ecotyper.nmf.NMFFit attribute) welch_t_test_p() (in module ecotyper.rcompat.stats) which_max() (in module ecotyper.rcompat.stats) write_discovery() (in module ecotyper.workflows) write_discovery_scrna() (in module ecotyper.workflows) write_ecotype_recovery() (in module ecotyper.rlayout) write_matrix() (in module ecotyper.rcompat.io) write_model_files() (in module ecotyper.model) write_recovery_output() (in module ecotyper.rlayout) write_state_recovery() (in module ecotyper.rlayout) write_table() (in module ecotyper.rcompat.io)