API for caravagnalab/basilica
bascule
| Global functions | |
|---|---|
| .onLoad | Source code |
| COSMIC_cn | Man page |
| COSMIC_color_palette | Source code |
| COSMIC_dbs | Man page |
| COSMIC_indels | Man page |
| COSMIC_sbs | Man page |
| COSMIC_sbs_filt | Man page |
| Degasperi_DBS | Man page |
| Degasperi_SBS | Man page |
| bascule | Man page |
| bascule-package | Man page |
| breast_data | Man page |
| check_conda | Source code |
| check_conda_env | Source code |
| check_python_deps | Source code |
| compare_sigs_inf_gt | Source code |
| compute_cross_entropy_aux | Source code |
| compute_likelihood | Source code |
| compute_penalized_bic | Source code |
| compute_penalty | Source code |
| compute_refinement_score_aux | Source code |
| configure_environment | Man page Source code |
| convert_dn_names | Man page Source code |
| create_conda_env | Source code |
| delete.signature_aux | Source code |
| empirical_centroids | Source code |
| filter_denovo | Source code |
| filter_sigs_low_expos | Source code |
| fit | Man page Source code |
| fit_clustering | Man page Source code |
| gen_palette | Source code |
| gen_palette_aux | Source code |
| get_G | Source code |
| get_K | Source code |
| get_assigned_missing | Source code |
| get_best_seed | Source code |
| get_beta_weights | Source code |
| get_centroids | Source code |
| get_cluster_assignments | Source code |
| get_cluster_labels | Source code |
| get_clusters_score | Source code |
| get_denovo_signames | Man page Source code |
| get_denovo_signatures | Man page Source code |
| get_exposure | Man page Source code |
| get_fittypes | Source code |
| get_fixed_signames | Man page Source code |
| get_fixed_signatures | Man page Source code |
| get_gradient_norms | Source code |
| get_input | Man page Source code |
| get_input_signames | Source code |
| get_input_signatures | Source code |
| get_list_from_py | Source code |
| get_list_from_py_aux | Source code |
| get_list_from_py_clustering | Source code |
| get_mixing_proportions | Source code |
| get_n_denovo | Source code |
| get_n_groups | Source code |
| get_samples | Source code |
| get_scores_CL | Source code |
| get_seed | Source code Source code |
| get_signames | Man page Source code |
| get_signatures | Man page Source code |
| get_signatures_aux | Source code |
| get_tested_Ks | Source code |
| get_tested_seeds | Source code |
| get_train_params_py | Source code |
| get_types | Source code |
| have_alternatives | Source code |
| have_conda | Source code |
| have_conda_env | Source code |
| have_groups | Source code |
| have_loaded_env | Man page Source code |
| have_python_deps | Man page Source code |
| install_miniconda_bascule | Source code |
| install_python_deps | Source code |
| load_conda_env | Man page Source code |
| long_to_wide | Source code |
| merge_clusters | Man page Source code |
| nmf_single_type | Source code |
| plot.bascule_obj | Man page Source code |
| plot_QC | Source code |
| plot_beta_star | Source code |
| plot_catalogue | Source code |
| plot_centroids | Man page |
| plot_cls_score_heatmap | Source code |
| plot_cluster_scores | Source code |
| plot_data | Man page Source code |
| plot_data_differences | Source code |
| plot_exposures | Man page Source code |
| plot_fit | Man page Source code |
| plot_gradient_norms | Man page Source code |
| plot_likelihoods | Source code |
| plot_losses | Source code |
| plot_mixture_weights | Source code |
| plot_posterior_probs | Man page Source code |
| plot_scores | Man page Source code |
| plot_signatures | Man page Source code |
| plot_similarity_reference | Man page Source code |
| print.bascule_obj | Man page Source code |
| pyfit | Source code |
| pyro_clustering | Source code |
| pyro_nmf | Source code |
| qc_linearCombination | Source code |
| recompute_scores | Source code |
| refine_denovo_signatures | Man page Source code |
| refinement_single_fit | Source code |
| reformat_contexts | Source code |
| remove_alternatives | Source code |
| rename_denovo_py | Source code |
| rename_dn_expos | Source code |
| rename_object | Source code |
| renormalize_denovo_thr | Source code |
| set_alternatives | Source code |
| set_attribute | Source code |
| set_denovo_signatures | Source code |
| set_exposures | Source code |
| set_fixed_signatures | Source code |
| set_nmf_init_params | Source code |
| solve_quadratic_optimization | Source code |
| solve_quadratic_optimization_aux | Source code |
| synthetic_data | Man page |
| using_conda_env | Source code |
| which_conda_env | Man page Source code |
| wide_to_long | Source code |
