Index

_

__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 bulkdgd.reproducibility 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) (bulkdgd.core.model.BulkDGD 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_seeds_state() (in module bulkdgd.reproducibility) get_significant_genes() (in module bulkdgd.analysis.dea) (in module bulkdgd.analysis.residuals) get_silhouette_score() (in module bulkdgd.core.metrics) get_statistics() (in module bulkdgd.analysis.dea)

I

impute() (bulkdgd.core.model.BulkDGD method) 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 bulkdgd.reproducibility

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) scaling_factor (bulkdgd.core.dataclasses.GeneExpressionDataset property) (bulkdgd.core.model.BulkDGD property) set_log_var() (bulkdgd.core.latents.GaussianMixtureModelLegacy method) set_means() (bulkdgd.core.latents.GaussianMixtureModelLegacy method) set_seeds() (in module bulkdgd.reproducibility) 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)