Files in lehner-lab/doubledeepms

Analysis scripts to reproduce the figures and results from doubleDeepPCA manuscript

R/doubledeepms.R R/doubledeepms_3did_comparisons.R R/doubledeepms__aa_properties_pca.R R/doubledeepms__aa_properties_pca_WT_loadings.R R/doubledeepms__aa_properties_pca_singles_loadings.R R/doubledeepms__allosteric_mutations_scatterplot.R R/doubledeepms__calculate_angle.R R/doubledeepms__create_dir.R R/doubledeepms__define_confident_free_energies.R R/doubledeepms__format_dir.R R/doubledeepms__fraction_bound.R R/doubledeepms__fraction_folded.R R/doubledeepms__get_model_results.R R/doubledeepms__get_reference_id.R R/doubledeepms__gg_color_hue.R R/doubledeepms__ggpairs_binhex.R R/doubledeepms__mann_whitney_U_wrapper.R R/doubledeepms__mann_whitney_U_wrapper_rand.R R/doubledeepms__minimum_interchain_distances_from_PDB.R R/doubledeepms__mochi__construct_feature_matrix.R R/doubledeepms__mochi__encode_genotypes.R R/doubledeepms__mochi__fit_tmodel_3state.R R/doubledeepms__mochi__load_fitness_for_model.R R/doubledeepms__mochi__remove_constant_positions.R R/doubledeepms__persite_energy_vs_distance_plot.R R/doubledeepms__plot_additive_trait_binding.R R/doubledeepms__plot_additive_trait_folding.R R/doubledeepms__plot_binding_site_ROC.R R/doubledeepms__plot_fitness_replicates_cor.R R/doubledeepms__plot_growth_validations.R R/doubledeepms__plot_heatmap.R R/doubledeepms__plot_heatmap_subset.R R/doubledeepms__plot_isochore_fraction_bound.R R/doubledeepms__plot_loadings.R R/doubledeepms__plot_model_performance.R R/doubledeepms__plot_mutation_distributions.R R/doubledeepms__plot_sturcture_examples_residues.R R/doubledeepms__plot_validation_scatter.R R/doubledeepms__predict_binding_fitness_from_folding_fitness.R R/doubledeepms__predict_fitness.R R/doubledeepms__predict_fitness_from_id.R R/doubledeepms__pvalue.R R/doubledeepms__relative_angle_from_PDB.R R/doubledeepms__secondary_structure_from_PDB.R R/doubledeepms__temperature_factor_from_PDB.R R/doubledeepms__tile_heatmap_wrapper.R R/doubledeepms_allostery_plots.R R/doubledeepms_allostery_scatterplots.R R/doubledeepms_binding_interface.R R/doubledeepms_downsampling_analysis.R R/doubledeepms_eve_comparisons.R R/doubledeepms_fit_thermo_model.R R/doubledeepms_fitness_heatmaps.R R/doubledeepms_fitness_plots.R R/doubledeepms_foldx_comparisons.R R/doubledeepms_free_energy_heatmaps.R R/doubledeepms_free_energy_scatterplots.R R/doubledeepms_interface_mechanisms.R R/doubledeepms_polyphen2_comparisons.R R/doubledeepms_protein_stability_plots.R R/doubledeepms_structure_metrics.R R/doubledeepms_thermo_model_results.R README.md man/doubledeepms.Rd man/doubledeepms_3did_comparisons.Rd man/doubledeepms__aa_properties_pca.Rd man/doubledeepms__aa_properties_pca_WT_loadings.Rd man/doubledeepms__aa_properties_pca_singles_loadings.Rd man/doubledeepms__allosteric_mutations_scatterplot.Rd man/doubledeepms__calculate_angle.Rd man/doubledeepms__create_dir.Rd man/doubledeepms__define_confident_free_energies.Rd man/doubledeepms__format_dir.Rd man/doubledeepms__fraction_bound.Rd man/doubledeepms__fraction_folded.Rd man/doubledeepms__get_model_results.Rd man/doubledeepms__get_reference_id.Rd man/doubledeepms__gg_color_hue.Rd man/doubledeepms__ggpairs_binhex.Rd man/doubledeepms__mann_whitney_U_wrapper.Rd man/doubledeepms__mann_whitney_U_wrapper_rand.Rd man/doubledeepms__minimum_interchain_distances_from_PDB.Rd man/doubledeepms__mochi__construct_feature_matrix.Rd man/doubledeepms__mochi__encode_genotypes.Rd man/doubledeepms__mochi__fit_tmodel_3state.Rd man/doubledeepms__mochi__load_fitness_for_model.Rd man/doubledeepms__mochi__remove_constant_positions.Rd man/doubledeepms__persite_energy_vs_distance_plot.Rd man/doubledeepms__plot_additive_trait_binding.Rd man/doubledeepms__plot_additive_trait_folding.Rd man/doubledeepms__plot_binding_site_ROC.Rd man/doubledeepms__plot_fitness_replicates_cor.Rd man/doubledeepms__plot_growth_validations.Rd man/doubledeepms__plot_heatmap.Rd man/doubledeepms__plot_heatmap_subset.Rd man/doubledeepms__plot_isochore_fraction_bound.Rd man/doubledeepms__plot_loadings.Rd man/doubledeepms__plot_model_performance.Rd man/doubledeepms__plot_mutation_distributions.Rd man/doubledeepms__plot_sturcture_examples_residues.Rd man/doubledeepms__plot_validation_scatter.Rd man/doubledeepms__predict_binding_fitness_from_folding_fitness.Rd man/doubledeepms__predict_fitness.Rd man/doubledeepms__predict_fitness_from_id.Rd man/doubledeepms__pvalue.Rd man/doubledeepms__relative_angle_from_PDB.Rd man/doubledeepms__secondary_structure_from_PDB.Rd man/doubledeepms__temperature_factor_from_PDB.Rd man/doubledeepms__tile_heatmap_wrapper.Rd man/doubledeepms_allostery_plots.Rd man/doubledeepms_allostery_scatterplots.Rd man/doubledeepms_binding_interface.Rd man/doubledeepms_downsampling_analysis.Rd man/doubledeepms_eve_comparisons.Rd man/doubledeepms_fit_thermo_model.Rd man/doubledeepms_fitness_heatmaps.Rd man/doubledeepms_fitness_plots.Rd man/doubledeepms_foldx_comparisons.Rd man/doubledeepms_free_energy_heatmaps.Rd man/doubledeepms_free_energy_scatterplots.Rd man/doubledeepms_interface_mechanisms.Rd man/doubledeepms_polyphen2_comparisons.Rd man/doubledeepms_protein_stability_plots.Rd man/doubledeepms_structure_metrics.Rd man/doubledeepms_thermo_model_results.Rd