Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | Y | Z A all_weights() (in module mofaflex.pl) B Bernoulli (class in mofaflex.likelihoods) C Constant (class in mofaflex.priors) covariates_factor_scatter() (in module mofaflex.pl) covariates_weight_scatter() (in module mofaflex.pl) D dask_chunksize_mb (mofaflex._core.settings.Settings attribute) DataGenerator (class in mofaflex.tl) description (mofaflex.FeatureSet attribute) E 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_covariates (mofaflex.priors.GaussianProcess attribute) (mofaflex.terms.MofaFlex attribute) factor_covariates_names (mofaflex.priors.GaussianProcess attribute) (mofaflex.terms.MofaFlex attribute) factor_gp_covariates() (in module mofaflex.pl) factor_gp_group_correlation (mofaflex.priors.GaussianProcess attribute) (mofaflex.terms.MofaFlex attribute) factor_gp_lengthscale (mofaflex.priors.GaussianProcess attribute) (mofaflex.terms.MofaFlex attribute) factor_gp_scale (mofaflex.priors.GaussianProcess attribute) (mofaflex.terms.MofaFlex attribute) factor_gp_smoothness() (in module mofaflex.pl) factor_names (mofaflex.terms.MofaFlex attribute) factor_order (mofaflex.terms.MofaFlex 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) fit() (mofaflex.MOFAFLEX method) from_dataframe() (mofaflex.FeatureSets class method) from_dict() (mofaflex.FeatureSets class method) from_gmt() (mofaflex.FeatureSets class method) G GaussianProcess (class in mofaflex.priors) generate() (mofaflex.tl.DataGenerator method) generate_missingness() (mofaflex.tl.DataGenerator method) get() (mofaflex._core.settings.Settings method) get_annotations() (mofaflex.priors.InformedHorseshoe method) (mofaflex.terms.MofaFlex method) get_dispersion() (mofaflex.likelihoods.NegativeBinomial method) (mofaflex.likelihoods.Normal method) (mofaflex.MOFAFLEX method) get_factor_gps() (mofaflex.priors.GaussianProcess method) (mofaflex.terms.MofaFlex method) get_factors() (mofaflex.terms.MofaFlex method) get_free_gpu_idx() (in module mofaflex.tl) get_noisy_mask() (mofaflex.tl.DataGenerator method) get_perturbation_effects() (mofaflex.priors.GSFA method) (mofaflex.terms.MofaFlex method) get_posterior_inclusion_probabilities() (mofaflex.priors.GSFA method) (mofaflex.terms.MofaFlex method) get_r2() (mofaflex.MOFAFLEX method) get_significant_annotations() (mofaflex.priors.InformedHorseshoe method) (mofaflex.terms.MofaFlex method) get_sparse_factor_probabilities() (mofaflex.priors.SpikeSlab method) (mofaflex.terms.MofaFlex method) get_sparse_weight_probabilities() (mofaflex.priors.SpikeSlab method) (mofaflex.terms.MofaFlex method) get_weight_gps() (mofaflex.priors.GaussianProcess method) (mofaflex.terms.MofaFlex method) get_weights() (mofaflex.terms.MofaFlex method) group_names (mofaflex.MOFAFLEX attribute) GSFA (class in mofaflex.priors) H Horseshoe (class in mofaflex.priors) I impute_data() (mofaflex.MOFAFLEX method) InformedHorseshoe (class in mofaflex.priors) K keep() (mofaflex.FeatureSets method) L Laplace (class in mofaflex.priors) likelihoods (mofaflex.MOFAFLEX attribute) (mofaflex.tl.DataGenerator attribute) load() (mofaflex.MOFAFLEX class method) M match() (in module mofaflex.tl) median_size (mofaflex.FeatureSets attribute) merge_pairs() (mofaflex.FeatureSets method) merge_similar() (mofaflex.FeatureSets method) missing_y (mofaflex.tl.DataGenerator attribute) module mofaflex.likelihoods mofaflex.pl mofaflex.priors mofaflex.terms mofaflex.tl MOFAFLEX (class in mofaflex) MofaFlex (class in mofaflex.terms) mofaflex.likelihoods module mofaflex.pl module mofaflex.priors module mofaflex.terms module mofaflex.tl 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.terms.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.terms.MofaFlex attribute) n_informed_factors (mofaflex.priors.InformedHorseshoe attribute) (mofaflex.terms.MofaFlex attribute) n_partially_shared_factors (mofaflex.tl.DataGenerator attribute) n_private_factors (mofaflex.tl.DataGenerator attribute) n_samples (mofaflex.MOFAFLEX attribute) (mofaflex.tl.DataGenerator attribute) n_samples_total (mofaflex.MOFAFLEX attribute) n_terms (mofaflex.MOFAFLEX attribute) n_total_factors (mofaflex.terms.MofaFlex attribute) n_views (mofaflex.MOFAFLEX attribute) (mofaflex.tl.DataGenerator attribute) name (mofaflex.FeatureSet attribute) (mofaflex.FeatureSets attribute) NegativeBinomial (class in mofaflex.likelihoods) nmf (mofaflex.tl.DataGenerator attribute) noisy_w_mask (mofaflex.tl.DataGenerator attribute) Normal (class in mofaflex.likelihoods) (class in mofaflex.priors) normalize() (mofaflex.tl.DataGenerator method) 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) R remove() (mofaflex.FeatureSets method) S sample_names (mofaflex.MOFAFLEX 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) SpikeSlab (class in mofaflex.priors) subset() (mofaflex.FeatureSet method) (mofaflex.FeatureSets method) T terms (mofaflex.MOFAFLEX attribute) 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) trim() (mofaflex.FeatureSets method) U use_dask (mofaflex._core.settings.Settings 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) warped_factor_covariates (mofaflex.priors.GaussianProcess attribute) (mofaflex.terms.MofaFlex attribute) warped_weight_covariates (mofaflex.priors.GaussianProcess attribute) (mofaflex.terms.MofaFlex attribute) weight_covariates (mofaflex.priors.GaussianProcess attribute) (mofaflex.terms.MofaFlex attribute) weight_covariates_names (mofaflex.priors.GaussianProcess attribute) (mofaflex.terms.MofaFlex attribute) weight_gp_covariates() (in module mofaflex.pl) weight_gp_group_correlation (mofaflex.priors.GaussianProcess attribute) (mofaflex.terms.MofaFlex attribute) weight_gp_lengthscale (mofaflex.priors.GaussianProcess attribute) (mofaflex.terms.MofaFlex attribute) weight_gp_scale (mofaflex.priors.GaussianProcess attribute) (mofaflex.terms.MofaFlex attribute) weight_gp_smoothness() (in module mofaflex.pl) weight_sparsity_histogram() (in module mofaflex.pl) weights() (in module mofaflex.pl) weights_covariate() (in module mofaflex.pl) Y y (mofaflex.tl.DataGenerator attribute) Z z (mofaflex.tl.DataGenerator attribute)