Index

B

BasicTrajectoryModule (class in ternadecov.trajectories)

bulk_raw_gex_mg (ternadecov.dataset.DeconvolutionDataset property) bulk_sample_names (ternadecov.dataset.DeconvolutionDataset property)

C

calculate_prediction_error() (in module ternadecov.evaluation) calculate_sample_prediction_error() (in module ternadecov.simulator) calculate_trajectory_prediction_error() (in module ternadecov.simulator)

cell_type_str_list (ternadecov.dataset.DeconvolutionDataset attribute) (ternadecov.dataset.SingleCellDataset attribute) cell_type_str_to_index_map (ternadecov.dataset.DeconvolutionDataset attribute) (ternadecov.dataset.SingleCellDataset attribute)

D

DeconvolutionDataset (class in ternadecov.dataset) DeconvolutionDatasetParametrization (class in ternadecov.parametrization) DeconvolutionDatatypeParametrization (class in ternadecov.parametrization)

DeconvolutionExporter (class in ternadecov.deconvolution_exporter) DeconvolutionPlotter (class in ternadecov.deconvolution_plotter) DeconvolutionWriter (class in ternadecov.deconvolution_writer) do_deconvolution() (in module ternadecov.cli_tools)

E

evaluate_deconvolution() (ternadecov.sensitivity_analyzer.SensitivityAnalyzer static method) evaluate_model() (in module ternadecov.evaluation)

evaluate_paramset() (in module ternadecov.evaluation) evaluate_with_trajectory() (in module ternadecov.evaluation) export_results() (ternadecov.deconvolution_exporter.DeconvolutionExporter method)

F

fit_model() (ternadecov.time_deconv.TimeRegularizedDeconvolutionModel method)

G

generate_anndata_from_sim() (in module ternadecov.simulator) generate_batch() (in module ternadecov.time_deconv) generate_posterior_samples() (in module ternadecov.plotting_functions) GeneSelector (class in ternadecov.gene_selector) get_argument_parser() (in module ternadecov.base_cli) get_composition_trajectories() (ternadecov.trajectories.BasicTrajectoryModule method) (ternadecov.trajectories.VGPTrajectoryModule method)

get_default_evaluation_param() (in module ternadecov.evaluation) get_iqr_from_posterior_samples() (in module ternadecov.plotting_functions) get_torch_device() (in module ternadecov.cli_tools) guide() (ternadecov.time_deconv.TimeRegularizedDeconvolutionModel method) (ternadecov.trajectories.BasicTrajectoryModule method) (ternadecov.trajectories.NonTrajectoryModule method) (ternadecov.trajectories.TrajectoryModule method) (ternadecov.trajectories.VGPTrajectoryModule method)

H

hypercluster_anndata() (in module ternadecov.hypercluster)

hypercluster_params (ternadecov.parametrization.DeconvolutionDatasetParametrization property)

L

legendre_coefficient_mat() (in module ternadecov.stats_helpers)

M

main() (in module ternadecov.base_cli) melt_tensor_to_pandas() (in module ternadecov.utils) model() (ternadecov.time_deconv.TimeRegularizedDeconvolutionModel method) (ternadecov.trajectories.BasicTrajectoryModule method) (ternadecov.trajectories.NonTrajectoryModule method) (ternadecov.trajectories.TrajectoryModule method) (ternadecov.trajectories.VGPTrajectoryModule method) module ternadecov ternadecov.base_cli ternadecov.cli_tools ternadecov.dataset ternadecov.deconvolution_exporter ternadecov.deconvolution_plotter ternadecov.deconvolution_writer ternadecov.evaluation ternadecov.gene_selector ternadecov.hypercluster ternadecov.parametrization ternadecov.plotting_functions ternadecov.sensitivity_analyzer ternadecov.simulator ternadecov.stats_helpers ternadecov.time_deconv ternadecov.trajectories ternadecov.utils

N

NegativeBinomialAltParam() (in module ternadecov.stats_helpers) NonTrajectoryModule (class in ternadecov.trajectories) num_cell_types (ternadecov.dataset.DeconvolutionDataset attribute) (ternadecov.dataset.SingleCellDataset attribute)

num_inducing_points (ternadecov.parametrization.TimeRegularizedDeconvolutionGPParametrization property) num_samples (ternadecov.dataset.DeconvolutionDataset attribute)

P

ParameterizedTrajectoryModule (class in ternadecov.trajectories) plot_beta_g_distribution() (ternadecov.deconvolution_plotter.DeconvolutionPlotter method) plot_composition_trajectories() (ternadecov.deconvolution_plotter.DeconvolutionPlotter method) plot_composition_trajectories_via_posterior_sampling() (ternadecov.deconvolution_plotter.DeconvolutionPlotter method) plot_gp_composition_trajectories() (ternadecov.deconvolution_plotter.DeconvolutionPlotter method) plot_loss() (ternadecov.deconvolution_plotter.DeconvolutionPlotter method) plot_phi_g_distribution() (ternadecov.deconvolution_plotter.DeconvolutionPlotter method)

plot_sample_compositions_boxplot() (ternadecov.deconvolution_plotter.DeconvolutionPlotter method) plot_sample_compositions_boxplot_confidence() (ternadecov.deconvolution_plotter.DeconvolutionPlotter method) plot_sample_compositions_scatter() (ternadecov.deconvolution_plotter.DeconvolutionPlotter method) plot_scan_trajectories() (ternadecov.sensitivity_analyzer.SensitivityAnalyzer static method) plot_simulated_proportions() (in module ternadecov.simulator) plot_summarized_cell_compositions() (ternadecov.deconvolution_plotter.DeconvolutionPlotter method) preproc_anndata_hypercluster() (in module ternadecov.hypercluster)

S

sample_composition_default() (ternadecov.time_deconv.TimeRegularizedDeconvolutionModel method) sample_linear_proportions() (in module ternadecov.simulator) sample_linear_trajectories() (in module ternadecov.simulator) sample_periodic_proportions() (in module ternadecov.simulator) sample_periodic_trajectories() (in module ternadecov.simulator) sample_sigmoid_proportions() (in module ternadecov.simulator) sample_sigmoid_trajectories() (in module ternadecov.simulator)

sample_trajectories() (in module ternadecov.simulator) scan_parameter() (ternadecov.sensitivity_analyzer.SensitivityAnalyzer static method) select_features() (ternadecov.gene_selector.GeneSelector static method) SensitivityAnalyzer (class in ternadecov.sensitivity_analyzer) sigmoid() (in module ternadecov.simulator) simulate_data() (in module ternadecov.simulator) SingleCellDataset (class in ternadecov.dataset) summarize_posterior_samples() (in module ternadecov.plotting_functions)

T

t_m (ternadecov.dataset.DeconvolutionDataset property) ternadecov module ternadecov.base_cli module ternadecov.cli_tools module ternadecov.dataset module ternadecov.deconvolution_exporter module ternadecov.deconvolution_plotter module ternadecov.deconvolution_writer module ternadecov.evaluation module ternadecov.gene_selector module ternadecov.hypercluster module

ternadecov.parametrization module ternadecov.plotting_functions module ternadecov.sensitivity_analyzer module ternadecov.simulator module ternadecov.stats_helpers module ternadecov.time_deconv module ternadecov.trajectories module ternadecov.utils module TimeRegularizedDeconvolutionGPParametrization (class in ternadecov.parametrization) TimeRegularizedDeconvolutionModel (class in ternadecov.time_deconv) TimeRegularizedDeconvolutionModelParametrization (class in ternadecov.parametrization) training (ternadecov.trajectories.ParameterizedTrajectoryModule attribute) (ternadecov.trajectories.VGPTrajectoryModule attribute) TrajectoryModule (class in ternadecov.trajectories)

V

VGPTrajectoryModule (class in ternadecov.trajectories)

W

w_hat_gc (ternadecov.dataset.DeconvolutionDataset attribute) (ternadecov.dataset.SingleCellDataset attribute) write_cell_compositions() (ternadecov.deconvolution_writer.DeconvolutionWriter method)

write_sample_composition_default() (ternadecov.time_deconv.TimeRegularizedDeconvolutionModel method) write_sample_compositions() (ternadecov.time_deconv.TimeRegularizedDeconvolutionModel method) write_sample_draws_quantiles() (ternadecov.deconvolution_writer.DeconvolutionWriter method) write_summarized_cell_compositions() (ternadecov.deconvolution_writer.DeconvolutionWriter method)