Index A | B | C | D | E | F | G | I | K | L | M | N | O | P | R | S | T | U | V | W | Y | Z A all_weights() (in module mofaflex.pl) annotation_confidence (mofaflex.ModelOptions attribute) annotations_varm_key (mofaflex.DataOptions attribute) B batch_size (mofaflex.TrainingOptions attribute) C covariates (mofaflex.MOFAFLEX attribute) covariates_factor_scatter() (in module mofaflex.pl) covariates_names (mofaflex.MOFAFLEX attribute) covariates_obs_key (mofaflex.DataOptions attribute) covariates_obsm_key (mofaflex.DataOptions attribute) D dask_chunksize_mb (mofaflex._core.settings.Settings attribute) DataGenerator (class in mofaflex.tl) DataOptions (class in mofaflex) description (mofaflex.FeatureSet attribute) device (mofaflex.TrainingOptions attribute) E early_stopper_patience (mofaflex.TrainingOptions attribute) empty (mofaflex.FeatureSet attribute) (mofaflex.FeatureSets attribute) eps (mofaflex._core.settings.Settings attribute) F factor() (in module mofaflex.pl) factor_correlation() (in module mofaflex.pl) (in module mofaflex.tl) factor_names (mofaflex.MOFAFLEX attribute) factor_order (mofaflex.MOFAFLEX attribute) factor_prior (mofaflex.ModelOptions attribute) factor_significance() (in module mofaflex.pl) factor_size_dist (mofaflex.tl.DataGenerator attribute) factor_size_params (mofaflex.tl.DataGenerator attribute) factor_sparsity_histogram() (in module mofaflex.pl) factors_covariate() (in module mofaflex.pl) factors_scatter() (in module mofaflex.pl) feature_names (mofaflex.MOFAFLEX attribute) feature_set_by_name (mofaflex.FeatureSets attribute) feature_sets (mofaflex.FeatureSets attribute) features (mofaflex.FeatureSet attribute) (mofaflex.FeatureSets attribute) FeatureSet (class in mofaflex) FeatureSets (class in mofaflex) filter() (mofaflex.FeatureSets method) find() (mofaflex.FeatureSets method) find_similar_pairs() (mofaflex.FeatureSets method) from_dataframe() (mofaflex.FeatureSets class method) from_dict() (mofaflex.FeatureSets class method) from_gmt() (mofaflex.FeatureSets class method) G generate() (mofaflex.tl.DataGenerator method) generate_missingness() (mofaflex.tl.DataGenerator method) get() (mofaflex._core.settings.Settings method) get_annotations() (mofaflex.MOFAFLEX method) get_dispersion() (mofaflex.MOFAFLEX method) get_factors() (mofaflex.MOFAFLEX method) get_free_gpu_idx() (in module mofaflex.tl) get_gps() (mofaflex.MOFAFLEX method) get_noisy_mask() (mofaflex.tl.DataGenerator method) get_r2() (mofaflex.MOFAFLEX method) get_significant_factor_annotations() (mofaflex.MOFAFLEX method) get_sparse_factor_probabilities() (mofaflex.MOFAFLEX method) get_sparse_weight_probabilities() (mofaflex.MOFAFLEX method) get_weights() (mofaflex.MOFAFLEX method) gp_covariate() (in module mofaflex.pl) gp_group_correlation (mofaflex.MOFAFLEX attribute) gp_lengthscale (mofaflex.MOFAFLEX attribute) gp_scale (mofaflex.MOFAFLEX attribute) group_by (mofaflex.DataOptions attribute) group_covar_rank (mofaflex.SmoothOptions attribute) group_names (mofaflex.MOFAFLEX attribute) guiding_vars_likelihoods (mofaflex.ModelOptions attribute) guiding_vars_obs_keys (mofaflex.DataOptions attribute) guiding_vars_scales (mofaflex.ModelOptions attribute) I impute_data() (mofaflex.MOFAFLEX method) independent_lengthscales (mofaflex.SmoothOptions attribute) init_factors (mofaflex.ModelOptions attribute) init_scale (mofaflex.ModelOptions attribute) K keep() (mofaflex.FeatureSets method) kernel (mofaflex.SmoothOptions attribute) L layer (mofaflex.DataOptions attribute) likelihoods (mofaflex.ModelOptions attribute) (mofaflex.tl.DataGenerator attribute) load() (mofaflex.MOFAFLEX class method) lr (mofaflex.TrainingOptions attribute) M match() (in module mofaflex.tl) max_epochs (mofaflex.TrainingOptions attribute) median_size (mofaflex.FeatureSets attribute) MEFISTO (in module mofaflex.presets) mefisto_kernel (mofaflex.SmoothOptions attribute) merge_pairs() (mofaflex.FeatureSets method) merge_similar() (mofaflex.FeatureSets method) missing_y (mofaflex.tl.DataGenerator attribute) ModelOptions (class in mofaflex) module mofaflex mofaflex.presets MOFA (in module mofaflex.presets) mofa_compat (mofaflex.TrainingOptions attribute) mofaflex module MOFAFLEX (class in mofaflex) mofaflex.presets module msigdb_get_features() (in module mofaflex.tl) msigdb_list_categories() (in module mofaflex.tl) msigdb_list_versions() (in module mofaflex.tl) N n_active_factors (mofaflex.tl.DataGenerator attribute) n_covariates (mofaflex.tl.DataGenerator attribute) n_factors (mofaflex.ModelOptions attribute) (mofaflex.MOFAFLEX attribute) (mofaflex.tl.DataGenerator attribute) n_features (mofaflex.MOFAFLEX attribute) (mofaflex.tl.DataGenerator attribute) n_features_total (mofaflex.MOFAFLEX attribute) n_fully_shared_factors (mofaflex.tl.DataGenerator attribute) n_groups (mofaflex.MOFAFLEX attribute) n_guided_factors (mofaflex.MOFAFLEX attribute) n_inducing (mofaflex.SmoothOptions attribute) n_informed_factors (mofaflex.MOFAFLEX attribute) n_partially_shared_factors (mofaflex.tl.DataGenerator attribute) n_particles (mofaflex.TrainingOptions attribute) n_private_factors (mofaflex.tl.DataGenerator attribute) n_samples (mofaflex.MOFAFLEX attribute) (mofaflex.tl.DataGenerator attribute) n_samples_total (mofaflex.MOFAFLEX attribute) n_uninformed_factors (mofaflex.MOFAFLEX attribute) n_views (mofaflex.MOFAFLEX attribute) (mofaflex.tl.DataGenerator attribute) name (mofaflex.FeatureSet attribute) (mofaflex.FeatureSets attribute) nmf (mofaflex.tl.DataGenerator attribute) noisy_w_mask (mofaflex.tl.DataGenerator attribute) nonnegative_factors (mofaflex.ModelOptions attribute) nonnegative_weights (mofaflex.ModelOptions attribute) normalize() (mofaflex.tl.DataGenerator method) NSF (in module mofaflex.presets) num_workers (mofaflex.TrainingOptions attribute) O override() (mofaflex._core.settings.Settings method) overview() (in module mofaflex.pl) P permute_factors() (mofaflex.tl.DataGenerator method) permute_features() (mofaflex.tl.DataGenerator method) pin_memory (mofaflex.TrainingOptions attribute) plot_data_overview (mofaflex.DataOptions attribute) R remove() (mofaflex.FeatureSets method) remove_constant_features (mofaflex.DataOptions attribute) S sample_names (mofaflex.MOFAFLEX attribute) save_path (mofaflex.TrainingOptions attribute) scale_per_group (mofaflex.DataOptions attribute) seed (mofaflex.TrainingOptions attribute) set() (mofaflex._core.settings.Settings method) Settings (class in mofaflex._core.settings) similarity_to_feature_sets() (mofaflex.FeatureSets method) similarity_to_observations() (mofaflex.FeatureSets method) smoothness() (in module mofaflex.pl) SmoothOptions (class in mofaflex) subset() (mofaflex.FeatureSet method) (mofaflex.FeatureSets method) subset_var (mofaflex.DataOptions attribute) T test_annotation_significance() (in module mofaflex.tl) to_dict() (mofaflex.FeatureSets method) to_gmt() (mofaflex.FeatureSets method) to_mask() (mofaflex.FeatureSets method) to_mudata() (mofaflex.tl.DataGenerator method) top_weights() (in module mofaflex.pl) training_curve() (in module mofaflex.pl) training_loss (mofaflex.MOFAFLEX attribute) TrainingOptions (class in mofaflex) trim() (mofaflex.FeatureSets method) U use_dask (mofaflex._core.settings.Settings attribute) use_obs (mofaflex.DataOptions attribute) use_var (mofaflex.DataOptions attribute) V variance_explained() (in module mofaflex.pl) view_names (mofaflex.MOFAFLEX attribute) W w (mofaflex.tl.DataGenerator attribute) w_mask (mofaflex.tl.DataGenerator attribute) warp_groups (mofaflex.SmoothOptions attribute) warp_interval (mofaflex.SmoothOptions attribute) warp_open_begin (mofaflex.SmoothOptions attribute) warp_open_end (mofaflex.SmoothOptions attribute) warp_reference_group (mofaflex.SmoothOptions attribute) warped_covariates (mofaflex.MOFAFLEX attribute) weight_prior (mofaflex.ModelOptions attribute) weight_sparsity_histogram() (in module mofaflex.pl) weights() (in module mofaflex.pl) Y y (mofaflex.tl.DataGenerator attribute) Z z (mofaflex.tl.DataGenerator attribute)