Index A | B | C | D | E | F | G | I | K | L | M | N | P | Q | R | S | T | U | V | W | X A adata (splisosm.hyptest_glmm.SplisosmGLMM attribute) (splisosm.hyptest_np.SplisosmNP attribute) add_ratio_layer() (in module splisosm.utils) apply_residual_op() (splisosm.kernel.FFTKernel method) B batch_size (splisosm.logger.PatienceLogger attribute) best_epoch (splisosm.logger.PatienceLogger attribute) best_loss (splisosm.logger.PatienceLogger attribute) best_params (splisosm.logger.PatienceLogger attribute) C clone() (splisosm.model.MultinomGLM method) (splisosm.model.MultinomGLMM method) compute_feature_summaries() (in module splisosm.utils) convergence (splisosm.logger.PatienceLogger attribute) counts_to_ratios() (in module splisosm.utils) covariate_names (splisosm.hyptest_fft.SplisosmFFT attribute) (splisosm.hyptest_glmm.SplisosmGLMM attribute) (splisosm.hyptest_np.SplisosmNP attribute) D data (splisosm.dataset.IsoDataset attribute) dataset (splisosm.dataset.IsoDataset attribute) datasets (splisosm.dataset.IsoDataset attribute) DENSE_THRESHOLD (splisosm.kernel.SpatialCovKernel attribute) design_mtx (splisosm.hyptest_fft.SplisosmFFT attribute) (splisosm.hyptest_glmm.SplisosmGLMM attribute) (splisosm.hyptest_np.SplisosmNP attribute) device (splisosm.kernel_gpr.GPyTorchKernelGPR attribute) E eigendecomposition() (splisosm.kernel.SpatialCovKernel method) eigenvalues() (splisosm.kernel.FFTKernel method) (splisosm.kernel.IdentityKernel method) (splisosm.kernel.SpatialCovKernel method) epoch (splisosm.logger.PatienceLogger attribute) epochs_without_improvement (splisosm.logger.PatienceLogger attribute) extract_counts_n_ratios() (in module splisosm.utils) extract_feature_summary() (splisosm.hyptest_fft.SplisosmFFT method) (splisosm.hyptest_glmm.SplisosmGLMM method) (splisosm.hyptest_np.SplisosmNP method) extract_gene_level_statistics() (in module splisosm.utils) F false_discovery_control() (in module splisosm.utils) FFTKernel (class in splisosm.kernel) FFTKernelGPR (class in splisosm.kernel_gpr) filtered_adata (splisosm.hyptest_glmm.SplisosmGLMM property) (splisosm.hyptest_np.SplisosmNP property) fit() (splisosm.hyptest_glmm.SplisosmGLMM method) (splisosm.model.MultinomGLM method) (splisosm.model.MultinomGLMM method) fit_kernel_gpr() (in module splisosm.kernel_gpr) fit_residuals() (splisosm.kernel_gpr.FFTKernelGPR method) (splisosm.kernel_gpr.GPyTorchKernelGPR method) (splisosm.kernel_gpr.KernelGPR method) (splisosm.kernel_gpr.SklearnKernelGPR method) fit_residuals_batch() (splisosm.kernel_gpr.FFTKernelGPR method) (splisosm.kernel_gpr.KernelGPR method) (splisosm.kernel_gpr.SklearnKernelGPR method) fit_residuals_cube() (splisosm.kernel_gpr.FFTKernelGPR method) fitting_configs (splisosm.model.MultinomGLM attribute) (splisosm.model.MultinomGLMM attribute) fitting_method (splisosm.model.MultinomGLM attribute) (splisosm.model.MultinomGLMM attribute) fitting_time (splisosm.model.MultinomGLM attribute) (splisosm.model.MultinomGLMM attribute) forward() (splisosm.model.MultinomGLM method) (splisosm.model.MultinomGLMM method) from_adjacency() (splisosm.kernel.SpatialCovKernel class method) from_config() (splisosm.kernel_gpr.SklearnKernelGPR class method) from_coordinates() (splisosm.kernel.SpatialCovKernel class method) G gene_name (splisosm.dataset.IsoDataset attribute) gene_names (splisosm.dataset.IsoDataset attribute) (splisosm.hyptest_fft.SplisosmFFT attribute) (splisosm.hyptest_glmm.SplisosmGLMM attribute) (splisosm.hyptest_np.SplisosmNP attribute) get_cov_sp() (in module splisosm.utils) get_dataloader() (splisosm.dataset.IsoDataset method) get_fitted_models() (splisosm.hyptest_glmm.SplisosmGLMM method) get_fitted_ratios_anndata() (splisosm.hyptest_glmm.SplisosmGLMM method) get_formatted_test_results() (splisosm.hyptest_fft.SplisosmFFT method) (splisosm.hyptest_glmm.SplisosmGLMM method) (splisosm.hyptest_np.SplisosmNP method) get_gene_model() (splisosm.hyptest_glmm.SplisosmGLMM method) get_isoform_ratio() (splisosm.model.MultinomGLM method) get_kernel_op() (splisosm.kernel_gpr.FFTKernelGPR method) (splisosm.kernel_gpr.KernelGPR method) (splisosm.kernel_gpr.SklearnKernelGPR method) get_params_iter() (splisosm.logger.PatienceLogger method) get_training_summary() (splisosm.hyptest_glmm.SplisosmGLMM method) GPyTorchKernelGPR (class in splisosm.kernel_gpr) group_by_n_iso (splisosm.dataset.IsoDataset attribute) group_gene_by_n_iso (splisosm.dataset.IsoDataset attribute) I IdentityKernel (class in splisosm.kernel) init_ratio (splisosm.model.MultinomGLMM attribute) inv_cov (splisosm.kernel.SpatialCovKernel attribute) IsoDataset (class in splisosm.dataset) K K_eigvals (splisosm.kernel.SpatialCovKernel attribute) K_eigvecs (splisosm.kernel.SpatialCovKernel attribute) K_sp (splisosm.kernel.SpatialCovKernel attribute) KernelGPR (class in splisosm.kernel_gpr) L linear_hsic_test() (in module splisosm.kernel_gpr) liu_sf() (in module splisosm.likelihood) load() (splisosm.hyptest_glmm.SplisosmGLMM static method) load_visium_probe() (in module splisosm.io) load_visium_sp_meta() (in module splisosm.io) load_visiumhd_probe() (in module splisosm.io) load_xenium_codeword() (in module splisosm.io) log() (splisosm.logger.PatienceLogger method) log_prob_fastdm() (in module splisosm.likelihood) log_prob_fastmult() (in module splisosm.likelihood) log_prob_fastmult_batched() (in module splisosm.likelihood) log_prob_fastmvn() (in module splisosm.likelihood) log_prob_fastmvn_batched() (in module splisosm.likelihood) loss_history (splisosm.logger.PatienceLogger property) lr (splisosm.kernel_gpr.GPyTorchKernelGPR attribute) M make_kernel_gpr() (in module splisosm.kernel_gpr) min_delta (splisosm.logger.PatienceLogger attribute) module splisosm splisosm.dataset splisosm.hyptest_fft splisosm.hyptest_glmm splisosm.hyptest_np splisosm.io splisosm.kernel splisosm.kernel_gpr splisosm.likelihood splisosm.logger splisosm.model splisosm.simulation splisosm.utils MultinomGLM (class in splisosm.model) MultinomGLMM (class in splisosm.model) N n (splisosm.kernel_gpr.FFTKernelGPR property) n_factors (splisosm.hyptest_fft.SplisosmFFT attribute) (splisosm.hyptest_glmm.SplisosmGLMM attribute) (splisosm.hyptest_np.SplisosmNP attribute) (splisosm.model.MultinomGLM attribute) n_genes (splisosm.dataset.IsoDataset attribute) (splisosm.hyptest_fft.SplisosmFFT attribute) (splisosm.hyptest_glmm.SplisosmGLMM attribute) (splisosm.hyptest_np.SplisosmNP attribute) (splisosm.model.MultinomGLM attribute) n_grid (splisosm.hyptest_fft.SplisosmFFT attribute) (splisosm.kernel.FFTKernel attribute) n_inducing (splisosm.kernel_gpr.GPyTorchKernelGPR attribute) (splisosm.kernel_gpr.SklearnKernelGPR attribute) n_isos (splisosm.model.MultinomGLM attribute) n_isos_per_gene (splisosm.dataset.IsoDataset attribute) (splisosm.hyptest_fft.SplisosmFFT attribute) (splisosm.hyptest_glmm.SplisosmGLMM attribute) (splisosm.hyptest_np.SplisosmNP attribute) n_iter (splisosm.kernel_gpr.GPyTorchKernelGPR attribute) n_spots (splisosm.dataset.IsoDataset attribute) (splisosm.hyptest_fft.SplisosmFFT attribute) (splisosm.hyptest_glmm.SplisosmGLMM attribute) (splisosm.hyptest_np.SplisosmNP attribute) (splisosm.model.MultinomGLM attribute) neighbor_degree (splisosm.kernel.FFTKernel attribute) nx (splisosm.kernel_gpr.FFTKernelGPR property) ny (splisosm.kernel_gpr.FFTKernelGPR property) P patience (splisosm.logger.PatienceLogger attribute) PatienceLogger (class in splisosm.logger) power_spectral_density_1d() (splisosm.kernel.FFTKernel method) precompute_shared_kernel() (splisosm.kernel_gpr.SklearnKernelGPR method) prepare_inputs_from_anndata() (in module splisosm.utils) Q Q (splisosm.kernel.SpatialCovKernel attribute) R rank() (splisosm.kernel.SpatialCovKernel method) realization() (splisosm.kernel.FFTKernel method) (splisosm.kernel.IdentityKernel method) (splisosm.kernel.SpatialCovKernel method) rho (splisosm.kernel.FFTKernel attribute) run_hsic_gc() (in module splisosm.utils) run_sparkx() (in module splisosm.utils) S save() (splisosm.hyptest_glmm.SplisosmGLMM method) sdata (splisosm.hyptest_fft.SplisosmFFT attribute) setup_data() (splisosm.hyptest_fft.SplisosmFFT method) (splisosm.hyptest_glmm.SplisosmGLMM method) (splisosm.hyptest_np.SplisosmNP method) (splisosm.model.MultinomGLM method) (splisosm.model.MultinomGLMM method) shape() (splisosm.kernel.SpatialCovKernel method) share_variance (splisosm.model.MultinomGLMM attribute) signal_bounds_fixed (splisosm.kernel_gpr.FFTKernelGPR property) (splisosm.kernel_gpr.GPyTorchKernelGPR property) (splisosm.kernel_gpr.SklearnKernelGPR property) simulate_isoform_counts() (in module splisosm.simulation) simulate_isoform_counts_single_gene() (in module splisosm.simulation) SklearnKernelGPR (class in splisosm.kernel_gpr) sp_kernel (splisosm.hyptest_fft.SplisosmFFT attribute) (splisosm.hyptest_glmm.SplisosmGLMM attribute) (splisosm.hyptest_np.SplisosmNP attribute) SpatialCovKernel (class in splisosm.kernel) spectrum (splisosm.kernel.FFTKernel attribute) splisosm module splisosm.dataset module splisosm.hyptest_fft module splisosm.hyptest_glmm module splisosm.hyptest_np module splisosm.io module splisosm.kernel module splisosm.kernel_gpr module splisosm.likelihood module splisosm.logger module splisosm.model module splisosm.simulation module splisosm.utils module SplisosmFFT (class in splisosm.hyptest_fft) SplisosmGLMM (class in splisosm.hyptest_glmm) SplisosmNP (class in splisosm.hyptest_np) square_trace() (splisosm.kernel.FFTKernel method) (splisosm.kernel.IdentityKernel method) (splisosm.kernel.SpatialCovKernel method) store_param_history (splisosm.logger.PatienceLogger attribute) T test_differential_usage() (splisosm.hyptest_fft.SplisosmFFT method) (splisosm.hyptest_glmm.SplisosmGLMM method) (splisosm.hyptest_np.SplisosmNP method) test_spatial_variability() (splisosm.hyptest_fft.SplisosmFFT method) (splisosm.hyptest_glmm.SplisosmGLMM method) (splisosm.hyptest_np.SplisosmNP method) tol_relative (splisosm.logger.PatienceLogger attribute) trace() (splisosm.kernel.FFTKernel method) (splisosm.kernel.IdentityKernel method) (splisosm.kernel.SpatialCovKernel method) U update_params_from_dict() (splisosm.model.MultinomGLM method) V var_fix_sigma (splisosm.model.MultinomGLMM attribute) var_prior_model (splisosm.model.MultinomGLMM attribute) var_prior_model_params (splisosm.model.MultinomGLMM attribute) var_sp_prop() (splisosm.model.MultinomGLMM method) var_total() (splisosm.model.MultinomGLMM method) W workers (splisosm.kernel.FFTKernel attribute) X xtKx() (splisosm.kernel.FFTKernel method) (splisosm.kernel.IdentityKernel method) (splisosm.kernel.SpatialCovKernel method) xtKx_approx() (splisosm.kernel.FFTKernel method) (splisosm.kernel.IdentityKernel method) (splisosm.kernel.SpatialCovKernel method) xtKx_exact() (splisosm.kernel.IdentityKernel method) (splisosm.kernel.SpatialCovKernel method)