Index

_

__init__() (core.dataclasses.GeneExpressionDataset method) (core.decoder.Decoder method) (core.latent.GaussianMixtureModel method) (core.latent.RepresentationLayer method) (core.model.BulkDGDModel method) (core.outputmodules.OutputModuleNBFeatureDispersion method) (core.outputmodules.OutputModuleNBFullDispersion method) (core.outputmodules.OutputModulePoisson method) (core.priors.GaussianPrior method) (core.priors.SoftballPrior method)

A

activation (core.outputmodules.OutputModuleNBFeatureDispersion property) (core.outputmodules.OutputModuleNBFullDispersion property) (core.outputmodules.OutputModulePoisson property)

analysis.dea module analysis.reduction module

B

BulkDGDModel (class in core.model)

C

cm_type (core.latent.GaussianMixtureModel property) core.dataclasses module core.decoder module core.latent module

core.model module core.outputmodules module core.priors module

D

data_exp (core.dataclasses.GeneExpressionDataset property) dec (core.model.BulkDGDModel property) Decoder (class in core.decoder) device (core.model.BulkDGDModel property)

dim (core.latent.GaussianMixtureModel property) (core.latent.RepresentationLayer property) (core.priors.GaussianPrior property) (core.priors.SoftballPrior property)

F

filter_by_metadata() (in module recount3) forward() (core.decoder.Decoder method) (core.latent.GaussianMixtureModel method) (core.latent.RepresentationLayer method) (core.outputmodules.OutputModuleNBFeatureDispersion method) (core.outputmodules.OutputModuleNBFullDispersion method) (core.outputmodules.OutputModulePoisson method)

G

GaussianMixtureModel (class in core.latent) GaussianPrior (class in core.priors) GeneExpressionDataset (class in core.dataclasses) genes (core.dataclasses.GeneExpressionDataset property) genes.util module get_gene_sums() (in module recount3) get_genes_attributes() (in module genes) get_log2_fold_changes() (in module analysis.dea)

get_metadata() (in module recount3) get_mixture_probs() (core.latent.GaussianMixtureModel method) get_p_values() (in module analysis.dea) get_prior_log_prob() (core.latent.GaussianMixtureModel method) get_probability_density() (core.model.BulkDGDModel method) get_q_values() (in module analysis.dea) get_query_string() (in module recount3) get_representations() (core.model.BulkDGDModel method) gmm (core.model.BulkDGDModel property)

I

input_dim (core.outputmodules.OutputModuleNBFeatureDispersion property) (core.outputmodules.OutputModuleNBFullDispersion property) (core.outputmodules.OutputModulePoisson property)

ioutil.__init__ module

L

load_config_genes() (in module ioutil) load_config_model() (in module ioutil) load_config_plot() (in module ioutil) load_config_rep() (in module ioutil) load_config_train() (in module ioutil) load_decoder_outputs() (in module ioutil) load_loss() (in module ioutil) load_representations() (in module ioutil) load_samples() (in module ioutil) load_samples_batches() (in module recount3) load_time() (in module ioutil) log_prob() (core.latent.GaussianMixtureModel method) (core.outputmodules.OutputModuleNBFeatureDispersion method) (core.outputmodules.OutputModuleNBFullDispersion method) (core.outputmodules.OutputModulePoisson method) (core.priors.GaussianPrior method) (core.priors.SoftballPrior method)

log_prob_mass() (core.outputmodules.OutputModuleNBFeatureDispersion static method) (core.outputmodules.OutputModuleNBFullDispersion static method) (core.outputmodules.OutputModulePoisson static method) log_r (core.outputmodules.OutputModuleNBFeatureDispersion property) log_var (core.latent.GaussianMixtureModel property) log_var_prior (core.latent.GaussianMixtureModel property) loss() (core.outputmodules.OutputModuleNBFeatureDispersion method) (core.outputmodules.OutputModuleNBFullDispersion method) (core.outputmodules.OutputModulePoisson method)

M

mean (core.priors.GaussianPrior property) mean_exp (core.dataclasses.GeneExpressionDataset property) means (core.latent.GaussianMixtureModel property) means_prior (core.latent.GaussianMixtureModel property) merge_gene_sums_and_metadata() (in module recount3) module analysis.dea analysis.reduction core.dataclasses core.decoder core.latent core.model core.outputmodules core.priors genes.util ioutil.__init__ plotting.plots recount3.util

N

n_comp (core.latent.GaussianMixtureModel property)

n_rep (core.latent.RepresentationLayer property)

O

options (core.latent.RepresentationLayer property) output_dim (core.outputmodules.OutputModuleNBFeatureDispersion property) (core.outputmodules.OutputModuleNBFullDispersion property) (core.outputmodules.OutputModulePoisson property)

OutputModuleNBFeatureDispersion (class in core.outputmodules) OutputModuleNBFullDispersion (class in core.outputmodules) OutputModulePoisson (class in core.outputmodules)

P

perform_dea() (in module analysis.dea) perform_kpca() (in module analysis.reduction) perform_mds() (in module analysis.reduction) perform_pca() (in module analysis.reduction) perform_tsne() (in module analysis.reduction) plot_2d_dim_red() (in module plotting)

plot_get_representations_time() (in module plotting) plot_multiple_2d_dim_red() (in module plotting.plots) plot_r_values_hist() (in module plotting) plotting.plots module preprocess_samples() (in module ioutil)

R

radius (core.priors.SoftballPrior property) recount3.util module RepresentationLayer (class in core.latent)

rescale() (core.latent.RepresentationLayer method) (core.outputmodules.OutputModuleNBFeatureDispersion static method) (core.outputmodules.OutputModuleNBFullDispersion static method) (core.outputmodules.OutputModulePoisson static method) rescale_pred_means() (core.model.BulkDGDModel static method)

S

sample() (core.outputmodules.OutputModuleNBFeatureDispersion method) (core.outputmodules.OutputModuleNBFullDispersion method) (core.outputmodules.OutputModulePoisson method) (core.priors.GaussianPrior method) (core.priors.SoftballPrior method) sample_new_points() (core.latent.GaussianMixtureModel method) sample_probs() (core.latent.GaussianMixtureModel method) samples (core.dataclasses.GeneExpressionDataset property)

save_decoder_outputs() (in module ioutil) save_loss() (in module ioutil) save_representations() (in module ioutil) save_samples() (in module ioutil) save_time() (in module ioutil) sharpness (core.priors.SoftballPrior property) SoftballPrior (class in core.priors) stddev (core.priors.GaussianPrior property)

T

train() (core.model.BulkDGDModel method)

W

weights (core.latent.GaussianMixtureModel property)

weights_prior (core.latent.GaussianMixtureModel property)

Z

z (core.latent.RepresentationLayer property)