Man pages for lehner-lab/doubledeepms
Analysis scripts to reproduce the figures and results from doubleDeepPCA manuscript
| doubledeepms | doubledeepms |
| doubledeepms_3did_comparisons | doubledeepms_3did_comparisons |
| doubledeepms__aa_properties_pca | doubledeepms__aa_properties_pca |
| doubledeepms__aa_properties_pca_singles_loadings | doubledeepms__aa_properties_pca_singles_loadings |
| doubledeepms__aa_properties_pca_WT_loadings | doubledeepms__aa_properties_pca_WT_loadings |
| doubledeepms__allosteric_mutations_scatterplot | doubledeepms__allosteric_mutations_scatterplot |
| doubledeepms_allostery_plots | doubledeepms_allostery_plots |
| doubledeepms_allostery_scatterplots | doubledeepms_allostery_scatterplots |
| doubledeepms_binding_interface | doubledeepms_binding_interface |
| doubledeepms__calculate_angle | doubledeepms__calculate_angle |
| doubledeepms__create_dir | doubledeepms__create_dir |
| doubledeepms__define_confident_free_energies | doubledeepms__define_confident_free_energies |
| doubledeepms_downsampling_analysis | doubledeepms_downsampling_analysis |
| doubledeepms_eve_comparisons | doubledeepms_eve_comparisons |
| doubledeepms_fitness_heatmaps | doubledeepms_fitness_heatmaps |
| doubledeepms_fitness_plots | doubledeepms_fitness_plots |
| doubledeepms_fit_thermo_model | doubledeepms_fit_thermo_model |
| doubledeepms_foldx_comparisons | doubledeepms_foldx_comparisons |
| doubledeepms__format_dir | doubledeepms__format_dir |
| doubledeepms__fraction_bound | doubledeepms__fraction_bound |
| doubledeepms__fraction_folded | doubledeepms__fraction_folded |
| doubledeepms_free_energy_heatmaps | doubledeepms_free_energy_heatmaps |
| doubledeepms_free_energy_scatterplots | doubledeepms_free_energy_scatterplots |
| doubledeepms__get_model_results | doubledeepms__get_model_results |
| doubledeepms__get_reference_id | doubledeepms__get_reference_id |
| doubledeepms__gg_color_hue | doubledeepms__gg_color_hue |
| doubledeepms__ggpairs_binhex | doubledeepms__ggpairs_binhex |
| doubledeepms_interface_mechanisms | doubledeepms_interface_mechanisms |
| doubledeepms__mann_whitney_U_wrapper | doubledeepms__mann_whitney_U_wrapper |
| doubledeepms__mann_whitney_U_wrapper_rand | doubledeepms__mann_whitney_U_wrapper_rand |
| doubledeepms__minimum_interchain_distances_from_PDB | doubledeepms__minimum_interchain_distances_from_PDB |
| doubledeepms__mochi__construct_feature_matrix | doubledeepms__mochi__construct_feature_matrix |
| doubledeepms__mochi__encode_genotypes | doubledeepms__mochi__encode_genotypes |
| doubledeepms__mochi__fit_tmodel_3state | doubledeepms__mochi__fit_tmodel_3state |
| doubledeepms__mochi__load_fitness_for_model | doubledeepms__mochi__load_fitness_for_model |
| doubledeepms__mochi__remove_constant_positions | doubledeepms__mochi__remove_constant_positions |
| doubledeepms__persite_energy_vs_distance_plot | doubledeepms__persite_energy_vs_distance_plot |
| doubledeepms__plot_additive_trait_binding | doubledeepms__plot_additive_trait_binding |
| doubledeepms__plot_additive_trait_folding | doubledeepms__plot_additive_trait_folding |
| doubledeepms__plot_binding_site_ROC | doubledeepms__plot_binding_site_ROC |
| doubledeepms__plot_fitness_replicates_cor | doubledeepms__plot_fitness_replicates_cor |
| doubledeepms__plot_growth_validations | doubledeepms__plot_fitness_replicates_cor |
| doubledeepms__plot_heatmap | doubledeepms__plot_heatmap |
| doubledeepms__plot_heatmap_subset | doubledeepms__plot_heatmap_subset |
| doubledeepms__plot_isochore_fraction_bound | doubledeepms__plot_isochore_fraction_bound |
| doubledeepms__plot_loadings | doubledeepms__plot_loadings |
| doubledeepms__plot_model_performance | doubledeepms__plot_model_performance |
| doubledeepms__plot_mutation_distributions | doubledeepms__plot_mutation_distributions |
| doubledeepms__plot_sturcture_examples_residues | doubledeepms__plot_sturcture_examples_residues |
| doubledeepms__plot_validation_scatter | doubledeepms__plot_validation_scatter |
| doubledeepms_polyphen2_comparisons | doubledeepms_polyphen2_comparisons |
| doubledeepms__predict_binding_fitness_from_folding_fitness | doubledeepms__predict_binding_fitness_from_folding_fitness |
| doubledeepms__predict_fitness | doubledeepms__predict_fitness |
| doubledeepms__predict_fitness_from_id | doubledeepms__predict_fitness_from_id |
| doubledeepms_protein_stability_plots | doubledeepms_protein_stability_plots |
| doubledeepms__pvalue | doubledeepms__pvalue |
| doubledeepms__relative_angle_from_PDB | doubledeepms__relative_angle_from_PDB |
| doubledeepms__secondary_structure_from_PDB | doubledeepms__secondary_structure_from_PDB |
| doubledeepms_structure_metrics | doubledeepms_structure_metrics |
| doubledeepms__temperature_factor_from_PDB | doubledeepms__temperature_factor_from_PDB |
| doubledeepms_thermo_model_results | doubledeepms_thermo_model_results |
| doubledeepms__tile_heatmap_wrapper | doubledeepms__tile_heatmap_wrapper |
