API for caravagnalab/lineaGT
lineaGT
| Global functions | |
|---|---|
| .onLoad | Source code |
| add_color_palette | Source code |
| add_growth_rates | Source code |
| add_muts_fit | Source code |
| add_parent | Source code |
| add_phylo | Source code |
| add_theta_to_vaf | Source code |
| add_time_0 | Source code |
| add_tp_int | Source code |
| add_vaf | Source code |
| check_conda | Source code |
| check_conda_env | Source code |
| check_cov_dimensions | Source code |
| check_dp | Source code |
| check_k_interval | Source code |
| check_lineages | Source code |
| check_max_k | Source code |
| check_muts_theta | Source code |
| check_params | Source code |
| check_python_deps | Source code |
| check_timepoints | Source code |
| check_vaf_dimensions | Source code |
| classifier | Source code |
| compute_IC | Source code |
| compute_density | Source code |
| configure_environment | Man page Source code |
| convert_tp | Source code |
| cov.df.example | Man page |
| create_conda_env | Source code |
| differentiation_tree | Source code |
| edges_to_matrix | Source code |
| estimate_mean_ISs | Source code |
| estimate_n_pops | Man page Source code |
| filter_dataset | Man page Source code |
| filter_edges | Source code |
| filter_muller_df | Source code |
| fit | Man page Source code |
| fit_cluster_viber | Source code |
| fit_growth_clones | Source code |
| fit_growth_rates | Man page Source code |
| fit_growth_utils | Source code |
| fit_mutations | Man page Source code |
| fit_phylogenies | Man page Source code |
| fit_singleK | Source code |
| fit_trees | Source code |
| fit_viber | Source code |
| fix_missing_tps | Source code |
| format_means_df | Source code |
| generate_synthetic_df | Source code |
| get_IC | Source code |
| get_ISs | Man page Source code |
| get_ISs_list | Source code |
| get_ISs_single_cluster | Source code |
| get_adj | Source code |
| get_all_unique_muts_labels | Source code |
| get_best_k | Source code |
| get_best_scores | Source code |
| get_binomial_theta_cluster | Source code |
| get_color_palette | Source code |
| get_colors | Source code |
| get_cov_dataframe | Man page Source code |
| get_covariance_Cholesky | Man page Source code |
| get_covariance_Sigma | Man page Source code |
| get_default_hyperparameters | Source code |
| get_dens_df | Source code |
| get_dens_params | Source code |
| get_desc_list | Source code |
| get_dimensions | Man page Source code |
| get_edges_muts | Source code |
| get_gradient_norms | Source code |
| get_growth_params | Source code |
| get_growth_rates | Source code |
| get_growth_rates_exp | Source code |
| get_growth_rates_log | Source code |
| get_growth_rates_long | Source code |
| get_highlight | Source code |
| get_hyperpar | Source code |
| get_labels | Man page Source code |
| get_lineages | Man page Source code |
| get_losses | Source code |
| get_mean | Man page Source code |
| get_mean_long | Source code |
| get_mean_wide | Source code |
| get_model | Source code |
| get_mrca_df | Source code |
| get_mrca_next_tp | Source code |
| get_muller_edges | Source code |
| get_muller_pop | Source code |
| get_muts_fit | Source code |
| get_next_tp | Source code |
| get_object | Source code |
| get_pairs | Source code |
| get_params | Source code |
| get_params_train | Source code |
| get_parent | Source code |
| get_parent_rate | Source code |
| get_pop_df | Source code |
| get_pop_muts | Source code |
| get_python_dataframe | Source code |
| get_python_params | Source code |
| get_regression_df | Source code |
| get_root | Source code |
| get_selection_df | Source code |
| get_sigma | Man page Source code |
| get_sim_dataset | Source code |
| get_sim_k_interval | Source code |
| get_simulation_object | Source code |
| get_time_spec_mrca | Source code |
| get_timepoints | Man page Source code |
| get_tp_to_int | Source code |
| get_trees | Source code |
| get_unique_labels | Man page Source code |
| get_unique_muts_labels | Man page Source code |
| get_vaf_dataframe | Man page Source code |
| get_variance_long | Source code |
| get_weights | Man page Source code |
| get_z_probs | Man page Source code |
| have_conda | Source code |
| have_conda_env | Source code |
| have_corrected_pops | Source code |
| have_growth_rates | Source code |
| have_loaded_env | Man page Source code |
| have_muts_fit | Source code |
| have_phylo_fits | Source code |
| have_pop_df | Source code |
| have_pop_df_muts | Source code |
| have_python_deps | Man page Source code |
| have_tp_int | Source code |
| have_vaf_df | Source code |
| highlight_palette | Source code |
| initialize_object | Source code |
| install_miniconda_lineagt | Source code |
| install_python_deps | Source code |
| is_desc_of | Source code |
| load_conda_env | Man page Source code |
| load_losses | Source code |
| load_params_gradients | Source code |
| long_to_wide_cov | Source code |
| long_to_wide_muts | Source code |
| lowest_common_acestor | Source code |
| map_timepoints_int | Source code |
| mullerplot_util | Source code |
| mutate_tp | Source code |
| my_ggplot_theme | Source code |
| plot.mvnmm | Man page Source code |
| plot_2D | Source code |
| plot_IC | Man page Source code |
| plot_differentiation_tree | Man page Source code |
| plot_gradient_norms | Man page Source code |
| plot_growth_rates | Man page Source code |
| plot_growth_regression | Man page Source code |
| plot_losses | Man page Source code |
| plot_marginal | Man page Source code |
| plot_marginal_lineage | Source code |
| plot_marginal_single_plot | Source code |
| plot_mixture_weights | Man page Source code |
| plot_mullerplot | Man page Source code |
| plot_phylogeny | Man page Source code |
| plot_scatter_density | Man page Source code |
| plot_vaf | Man page Source code |
| plot_vaf_2D | Source code |
| plot_vaf_time | Man page Source code |
| pop_df_add_empty | Source code |
| posterior_samples_to_df | Source code |
| print.mvnmm | Man page Source code |
| replace_labels_muts | Source code |
| run_ctree | Source code |
| run_inference | Source code |
| run_py_growth | Source code |
| select_relevant_clusters | Source code |
| sort_clusters_edges | Source code |
| split_to_camelcase | Source code |
| update_color_palette | Source code |
| update_params | Source code |
| using_conda_env | Source code |
| util_plot_diff | Source code |
| vaf.df.example | Man page |
| which_conda_env | Man page Source code |
| wide_to_long_cov | Source code |
| wide_to_long_muts | Source code |
| x.example | Man page |
