Index _ | A | B | C | D | E | F | G | I | L | M | N | O | P | R | S | T | W | Z _ __init__() (bulkdgd.core.dataclasses.GeneExpressionDataset method) (bulkdgd.core.decoders.Decoder method) (bulkdgd.core.model.BulkDGD method) (bulkdgd.core.outputmodules.OutputModuleBase method) (bulkdgd.core.outputmodules.OutputModuleNBFeatureDispersion method) (bulkdgd.core.outputmodules.OutputModuleNBFullDispersion method) (bulkdgd.core.outputmodules.OutputModulePoisson method) (bulkdgd.core.priors.GaussianPrior method) (bulkdgd.core.priors.SoftballPrior method) A activation (bulkdgd.core.outputmodules.OutputModuleBase property) (bulkdgd.core.outputmodules.OutputModuleNBFeatureDispersion property) (bulkdgd.core.outputmodules.OutputModuleNBFullDispersion property) (bulkdgd.core.outputmodules.OutputModulePoisson property) B BulkDGD (class in bulkdgd.core.model) bulkdgd.analysis.dea module bulkdgd.analysis.reduction module bulkdgd.analysis.residuals module bulkdgd.core.dataclasses module bulkdgd.core.decoders module bulkdgd.core.latents module bulkdgd.core.metrics module bulkdgd.core.model module bulkdgd.core.outputmodules module bulkdgd.core.priors module bulkdgd.genes.util module bulkdgd.ioutil module bulkdgd.plotting.plots module C covariance_type (bulkdgd.core.latents.GaussianMixtureModelLegacy property) D data_exp (bulkdgd.core.dataclasses.GeneExpressionDataset property) decoder (bulkdgd.core.model.BulkDGD property) Decoder (class in bulkdgd.core.decoders) device (bulkdgd.core.latents.RepresentationLayer property) (bulkdgd.core.model.BulkDGD property) dim (bulkdgd.core.latents.GaussianMixtureModelLegacy property) (bulkdgd.core.latents.GaussianMixtureModelTGMM property) (bulkdgd.core.latents.RepresentationLayer property) (bulkdgd.core.priors.GaussianPrior property) (bulkdgd.core.priors.SoftballPrior property) E encode_labels() (in module bulkdgd.core.metrics) F forward() (bulkdgd.core.decoders.Decoder method) (bulkdgd.core.latents.GaussianMixtureModelLegacy method) (bulkdgd.core.latents.GaussianMixtureModelTGMM method) (bulkdgd.core.latents.RepresentationLayer method) (bulkdgd.core.outputmodules.OutputModuleNBFeatureDispersion method) (bulkdgd.core.outputmodules.OutputModuleNBFullDispersion method) (bulkdgd.core.outputmodules.OutputModulePoisson method) G GaussianMixtureModelLegacy (class in bulkdgd.core.latents) GaussianMixtureModelTGMM (class in bulkdgd.core.latents) GaussianPrior (class in bulkdgd.core.priors) GeneExpressionDataset (class in bulkdgd.core.dataclasses) genes (bulkdgd.core.dataclasses.GeneExpressionDataset property) get_adjusted_mutual_info_score() (in module bulkdgd.core.metrics) get_adjusted_rand_score() (in module bulkdgd.core.metrics) get_bic_score() (in module bulkdgd.core.metrics) get_calinski_harabasz_score() (in module bulkdgd.core.metrics) get_davies_bouldin_score() (in module bulkdgd.core.metrics) get_enrichment_scores() (in module bulkdgd.analysis.dea) get_genes_attributes() (in module bulkdgd.genes.util) get_genes_by_residual_threshold() (in module bulkdgd.analysis.residuals) get_log2_fold_changes() (in module bulkdgd.analysis.dea) get_metric_optimization_direction() (in module bulkdgd.core.metrics) get_metric_score() (in module bulkdgd.core.metrics) get_mixture_probs() (bulkdgd.core.latents.GaussianMixtureModelLegacy method) (bulkdgd.core.latents.GaussianMixtureModelTGMM method) get_normalized_mutual_info_score() (in module bulkdgd.core.metrics) get_p_values() (in module bulkdgd.analysis.dea) get_prior_log_prob() (bulkdgd.core.latents.GaussianMixtureModelLegacy method) get_probability_density() (bulkdgd.core.model.BulkDGD method) get_q_values() (in module bulkdgd.analysis.dea) get_representations() (bulkdgd.core.model.BulkDGD method) get_residuals() (in module bulkdgd.analysis.residuals) get_significant_genes() (in module bulkdgd.analysis.dea) (in module bulkdgd.analysis.residuals) get_silhouette_score() (in module bulkdgd.core.metrics) I input_dim (bulkdgd.core.outputmodules.OutputModuleBase property) (bulkdgd.core.outputmodules.OutputModuleNBFeatureDispersion property) (bulkdgd.core.outputmodules.OutputModuleNBFullDispersion property) (bulkdgd.core.outputmodules.OutputModulePoisson property) L latent (bulkdgd.core.model.BulkDGD property) load() (bulkdgd.core.latents.RepresentationLayer class method) load_config_dim_red() (in module bulkdgd.ioutil) load_config_genes() (in module bulkdgd.ioutil) load_config_model() (in module bulkdgd.ioutil) load_config_plot() (in module bulkdgd.ioutil) load_config_rep() (in module bulkdgd.ioutil) load_config_train() (in module bulkdgd.ioutil) load_decoder_outputs() (in module bulkdgd.ioutil) load_representations() (in module bulkdgd.ioutil) load_samples() (in module bulkdgd.ioutil) load_state_dict() (bulkdgd.core.latents.GaussianMixtureModelTGMM method) log_prob() (bulkdgd.core.latents.GaussianMixtureModelLegacy method) (bulkdgd.core.latents.GaussianMixtureModelTGMM method) (bulkdgd.core.outputmodules.OutputModuleNBFeatureDispersion method) (bulkdgd.core.outputmodules.OutputModuleNBFullDispersion method) (bulkdgd.core.outputmodules.OutputModulePoisson method) (bulkdgd.core.priors.GaussianPrior method) (bulkdgd.core.priors.SoftballPrior method) log_prob_mass() (bulkdgd.core.outputmodules.OutputModuleNBFeatureDispersion static method) (bulkdgd.core.outputmodules.OutputModuleNBFullDispersion static method) (bulkdgd.core.outputmodules.OutputModulePoisson static method) log_r (bulkdgd.core.outputmodules.OutputModuleNBFeatureDispersion property) log_var (bulkdgd.core.latents.GaussianMixtureModelLegacy property) log_var_prior (bulkdgd.core.latents.GaussianMixtureModelLegacy property) loss() (bulkdgd.core.outputmodules.OutputModuleNBFeatureDispersion method) (bulkdgd.core.outputmodules.OutputModuleNBFullDispersion method) (bulkdgd.core.outputmodules.OutputModulePoisson method) M mean (bulkdgd.core.priors.GaussianPrior property) mean_exp (bulkdgd.core.dataclasses.GeneExpressionDataset property) means (bulkdgd.core.latents.GaussianMixtureModelLegacy property) (bulkdgd.core.latents.GaussianMixtureModelTGMM property) means_prior (bulkdgd.core.latents.GaussianMixtureModelLegacy property) module bulkdgd.analysis.dea bulkdgd.analysis.reduction bulkdgd.analysis.residuals bulkdgd.core.dataclasses bulkdgd.core.decoders bulkdgd.core.latents bulkdgd.core.metrics bulkdgd.core.model bulkdgd.core.outputmodules bulkdgd.core.priors bulkdgd.genes.util bulkdgd.ioutil bulkdgd.plotting.plots N n_components (bulkdgd.core.latents.GaussianMixtureModelLegacy property) n_rep (bulkdgd.core.latents.RepresentationLayer property) O options (bulkdgd.core.latents.RepresentationLayer property) output_dim (bulkdgd.core.outputmodules.OutputModuleBase property) (bulkdgd.core.outputmodules.OutputModuleNBFeatureDispersion property) (bulkdgd.core.outputmodules.OutputModuleNBFullDispersion property) (bulkdgd.core.outputmodules.OutputModulePoisson property) OutputModuleBase (class in bulkdgd.core.outputmodules) OutputModuleNBFeatureDispersion (class in bulkdgd.core.outputmodules) OutputModuleNBFullDispersion (class in bulkdgd.core.outputmodules) OutputModulePoisson (class in bulkdgd.core.outputmodules) P perform_dea() (in module bulkdgd.analysis.dea) perform_kpca() (in module bulkdgd.analysis.reduction) perform_mds() (in module bulkdgd.analysis.reduction) perform_pca() (in module bulkdgd.analysis.reduction) perform_tsne() (in module bulkdgd.analysis.reduction) perform_umap() (in module bulkdgd.analysis.reduction) plot_dimensionality_reduction() (in module bulkdgd.plotting.plots) plot_enrichment_scores() (in module bulkdgd.plotting.plots) plot_representations_time() (in module bulkdgd.plotting.plots) plot_rvalues() (in module bulkdgd.plotting.plots) preprocess_samples() (in module bulkdgd.ioutil) R radius (bulkdgd.core.priors.SoftballPrior property) RepresentationLayer (class in bulkdgd.core.latents) rescale() (bulkdgd.core.latents.RepresentationLayer method) (bulkdgd.core.outputmodules.OutputModuleNBFeatureDispersion static method) (bulkdgd.core.outputmodules.OutputModuleNBFullDispersion static method) (bulkdgd.core.outputmodules.OutputModulePoisson static method) rescale_pred_means() (bulkdgd.core.model.BulkDGD static method) S sample() (bulkdgd.core.outputmodules.OutputModuleNBFeatureDispersion method) (bulkdgd.core.outputmodules.OutputModuleNBFullDispersion method) (bulkdgd.core.outputmodules.OutputModulePoisson method) (bulkdgd.core.priors.GaussianPrior method) (bulkdgd.core.priors.SoftballPrior method) sample_new_points() (bulkdgd.core.latents.GaussianMixtureModelLegacy method) (bulkdgd.core.latents.GaussianMixtureModelTGMM method) sample_probs() (bulkdgd.core.latents.GaussianMixtureModelLegacy method) (bulkdgd.core.latents.GaussianMixtureModelTGMM method) samples (bulkdgd.core.dataclasses.GeneExpressionDataset property) save() (bulkdgd.core.latents.GaussianMixtureModelLegacy method) (bulkdgd.core.latents.RepresentationLayer method) save_decoder_outputs() (in module bulkdgd.ioutil) save_representations() (in module bulkdgd.ioutil) save_samples() (in module bulkdgd.ioutil) set_log_var() (bulkdgd.core.latents.GaussianMixtureModelLegacy method) set_means() (bulkdgd.core.latents.GaussianMixtureModelLegacy method) set_weights() (bulkdgd.core.latents.GaussianMixtureModelLegacy method) sharpness (bulkdgd.core.priors.SoftballPrior property) SoftballPrior (class in bulkdgd.core.priors) state_dict() (bulkdgd.core.latents.GaussianMixtureModelTGMM method) stddev (bulkdgd.core.priors.GaussianPrior property) T to() (bulkdgd.core.latents.GaussianMixtureModelTGMM method) train() (bulkdgd.core.model.BulkDGD method) W weights (bulkdgd.core.latents.GaussianMixtureModelLegacy property) (bulkdgd.core.latents.GaussianMixtureModelTGMM property) weights_prior (bulkdgd.core.latents.GaussianMixtureModelLegacy property) Z z (bulkdgd.core.latents.RepresentationLayer property)