├── .gitattributes ├── .gitignore ├── LICENSE.md ├── MaveDB_upload ├── mavedb_upload.Rmd ├── mavedb_upload.md ├── score-set_binding_bc.csv ├── score-set_binding_mut.csv ├── score-set_expression_bc.csv └── score-set_expression_mut.csv ├── README.md ├── SRA_upload ├── .gitignore ├── README.md ├── SRA_submission_spreadsheet.tsv └── upload_to_SRA.ipynb ├── Snakefile ├── analyze_counts.ipynb ├── antibody_epitopes.Rmd ├── circulating_variants.Rmd ├── cluster.yaml ├── compute_binding_Kd.Rmd ├── compute_expression_meanF.Rmd ├── config.yaml ├── count_variants.ipynb ├── data ├── PacBio_amplicons.gb ├── PacBio_runs.csv ├── RBD_sites.csv ├── README.md ├── alignments │ ├── RBD_nt_tree │ │ ├── RAxML_bestTree.RBD_nt_tree.txt │ │ ├── RAxML_bipartitions.RBD_nt_tree.txt │ │ ├── RAxML_bipartitionsBranchLabels.RBD_nt_tree.txt │ │ ├── RAxML_bootstrap.RBD_nt_tree.txt │ │ └── RAxML_info.RBD_nt_tree.txt │ ├── RBD_tree │ │ ├── RAxML_bestTree.RBD_tree.txt │ │ ├── RAxML_bipartitions.RBD_tree.txt │ │ ├── RAxML_bipartitionsBranchLabels.RBD_tree.txt │ │ ├── RAxML_bootstrap.RBD_tree.txt │ │ └── RAxML_info.RBD_tree.txt │ ├── RBDs_aligned.fasta │ ├── RBDs_nt_aligned.fasta │ ├── Spike_GISAID │ │ ├── gisaid_hcov-19_acknowledgement_table.xls │ │ ├── spike_GISAID_aligned.fasta │ │ ├── spikeprot0527.fasta │ │ ├── spikeprot0527.zip │ │ └── unzip-and-align.sh │ ├── Spike_nt_tree │ │ ├── RAxML_bestTree.Spike_nt_tree.txt │ │ ├── RAxML_bipartitions.Spike_nt_tree.txt │ │ ├── RAxML_bipartitionsBranchLabels.Spike_nt_tree.txt │ │ ├── RAxML_bootstrap.Spike_nt_tree.txt │ │ └── RAxML_info.Spike_nt_tree.txt │ ├── Spike_tree │ │ ├── RAxML_bestTree.Spike_tree.txt │ │ ├── RAxML_bipartitions.Spike_tree.txt │ │ ├── RAxML_bipartitionsBranchLabels.Spike_tree.txt │ │ ├── RAxML_bootstrap.Spike_tree.txt │ │ └── RAxML_info.Spike_tree.txt │ ├── Spikes_aligned.fasta │ ├── Spikes_nt_aligned.fasta │ ├── alignment-and-phylogeny.sh │ └── unaligned-sequences │ │ ├── RBDs.fasta │ │ ├── RBDs_nt.fasta │ │ ├── Spikes.fasta │ │ ├── Spikes_nt.fasta │ │ └── old │ │ ├── RBDs.fasta │ │ └── Spikes.fasta ├── barcode_runs.csv ├── barcode_runs_orig-names.csv ├── build_barcode_runs.ipynb ├── feature_parse_specs.yaml ├── isogenic_titrations │ ├── Table-all.csv │ ├── homolog_validations.Rmd │ ├── homolog_validations.csv │ ├── homolog_validations.md │ ├── homolog_validations_files │ │ └── figure-gfm │ │ │ ├── expression_plots-1.png │ │ │ ├── titrations_plot_homolog_panel-1.png │ │ │ └── wildtype_triplicate_titrations_plot-1.png │ ├── isogenic_titrations_files │ │ └── figure-gfm │ │ │ ├── expression_plots-1.png │ │ │ ├── titrations_plot_homolog_panel-1.png │ │ │ └── wildtype_triplicate_titrations_plot-1.png │ ├── point-mut-validations.Rmd │ ├── point-mut-validations.csv │ ├── point-mut-validations.md │ ├── point-mut-validations_files │ │ └── figure-gfm │ │ │ ├── alt_expression_plots-1.png │ │ │ ├── expression_plots-1.png │ │ │ ├── plot_by_category-1.png │ │ │ └── plot_point_mut_panel-1.png │ ├── pseudovirus_titer.Rmd │ ├── pseudovirus_titer.md │ ├── pseudovirus_titer_files │ │ └── figure-gfm │ │ │ ├── unnamed-chunk-2-1.svg │ │ │ └── unnamed-chunk-3-1.svg │ ├── pseudovirus_titers.csv │ └── results │ │ ├── homolog_FITC_expression.pdf │ │ ├── homolog_titration.pdf │ │ ├── isogenic_titrations_summary.csv │ │ ├── point-mut_FITC_expression.pdf │ │ ├── point-mut_FITC_expression_mean-SE.pdf │ │ ├── point-mut_titration.pdf │ │ ├── point-mut_titration_multiple.pdf │ │ ├── point_mutants_summary.csv │ │ ├── stringent_titers.pdf │ │ ├── stringent_titers_p24_normalized.pdf │ │ ├── titers.pdf │ │ └── wildtype_triplicate_titration.pdf ├── lit-measurements │ └── Letko_2020_data.csv ├── plasmid_maps │ ├── 2649_pETcon-SARS-CoV-2-RBD-201aa.gb │ ├── 2649lib_pETcon-SARS-CoV-2-RBD-201aa_lib-assembled.gb │ └── 2736_HDM_IDTSpike_EcoKozak.gb ├── primers │ ├── mutational_lib │ │ ├── 2649_o29-o70-amplicon.ape │ │ ├── IDT-order.xlsx │ │ ├── README.md │ │ ├── SARS-CoV-2_RBD.txt │ │ ├── SARS-CoV-2_RBD_NNSprimers.txt │ │ ├── SARS-CoV-2_RBD_NNSprimers_for.txt │ │ ├── SARS-CoV-2_RBD_NNSprimers_rev.txt │ │ └── create_NNSprimers_py3.py │ └── primers.csv ├── structures │ ├── ACE2-bound │ │ ├── 2ajf.pdb │ │ ├── 6m0j.pdb │ │ ├── 6m0j_no-ACE2.pdb │ │ ├── 6m17.pdb │ │ ├── 6vsb.pdb │ │ ├── 6vxx.pdb │ │ └── 6vyb.pdb │ ├── Ab-bound │ │ ├── 80R_2ghw.pdb │ │ ├── B38_7bz5.pdb │ │ ├── CR3022_6w41.pdb │ │ ├── F26G19_3bgf.pdb │ │ ├── S230_6nb6.pdb │ │ ├── S230_6nb7.pdb │ │ ├── S309_6wps.pdb │ │ ├── VHH-72_6waq.pdb │ │ └── m396_2dd8.pdb │ ├── RBD_sites_input.csv │ └── annotate-structural-elements.R └── uni-sans │ ├── Uni Sans Heavy Italic.otf │ ├── Uni Sans Heavy.otf │ ├── Uni Sans Thin Italic.otf │ └── Uni Sans Thin.otf ├── docs ├── .gitignore ├── 404.html ├── Gemfile ├── Gemfile.lock ├── _config.yml ├── _includes │ └── interactive_heatmap.html ├── _layouts │ ├── default.html │ └── dms-view.html ├── index.md └── structures.md ├── environment.yml ├── environment_unpinned.yml ├── global_epistasis_binding.ipynb ├── global_epistasis_expression.ipynb ├── interactive_heatmap.ipynb ├── logomaker_utils.py ├── logoplots_of_muteffects.ipynb ├── process_ccs.ipynb ├── results ├── binding_Kds │ ├── binding_Kds.csv │ └── binding_Kds_homologs.csv ├── counts │ └── variant_counts.csv ├── dms_view │ ├── README.md │ ├── description_RBD.md │ ├── description_spike.md │ ├── dms-view_table_RBD.csv │ └── dms-view_table_spike.csv ├── expression_meanFs │ ├── expression_meanFs.csv │ └── expression_meanFs_homologs.csv ├── single_mut_effects │ ├── homolog_effects.csv │ └── single_mut_effects.csv ├── structure_function │ ├── 6m0j_b-factor-mean-bind.pdb │ └── 6m0j_b-factor-mean-expr.pdb ├── summary │ ├── analyze_counts.md │ ├── analyze_counts_files │ │ ├── analyze_counts_23_0.png │ │ ├── analyze_counts_25_0.png │ │ ├── analyze_counts_27_0.png │ │ ├── analyze_counts_29_0.png │ │ ├── analyze_counts_31_0.png │ │ ├── analyze_counts_33_0.png │ │ ├── analyze_counts_33_1.png │ │ ├── analyze_counts_33_2.png │ │ ├── analyze_counts_33_3.png │ │ ├── analyze_counts_33_4.png │ │ ├── analyze_counts_33_5.png │ │ ├── analyze_counts_33_6.png │ │ └── analyze_counts_33_7.png │ ├── antibody_epitopes.md │ ├── antibody_epitopes_files │ │ └── figure-gfm │ │ │ ├── escape_mut_tol_per_mut-1.png │ │ │ ├── escape_mut_tol_per_site-1.png │ │ │ ├── heatmaps_epitope_mut_effects_RBM_mAbs-1.png │ │ │ ├── heatmaps_epitope_mut_effects_core_mAbs-1.png │ │ │ ├── natural_diversity_epitopes-1.png │ │ │ ├── scatterplot_epitope_mut_effects-1.png │ │ │ └── violin_plot_epitope_mut_effects-1.png │ ├── build_variants.md │ ├── build_variants_files │ │ ├── build_variants_22_0.png │ │ ├── build_variants_26_0.png │ │ ├── build_variants_28_0.png │ │ ├── build_variants_30_0.png │ │ ├── build_variants_34_0.png │ │ ├── build_variants_40_1.png │ │ ├── build_variants_49_0.png │ │ ├── build_variants_51_1.png │ │ ├── build_variants_53_2.png │ │ ├── build_variants_65_0.png │ │ ├── build_variants_73_0.png │ │ ├── build_variants_75_1.png │ │ ├── build_variants_75_2.png │ │ ├── build_variants_77_1.png │ │ ├── build_variants_79_0.png │ │ ├── build_variants_81_1.png │ │ ├── build_variants_81_2.png │ │ ├── build_variants_85_0.png │ │ ├── build_variants_85_1.png │ │ ├── build_variants_87_0.png │ │ └── build_variants_87_1.png │ ├── circulating_variants.md │ ├── circulating_variants_files │ │ └── figure-gfm │ │ │ ├── circulating_variant_DFEs-1.png │ │ │ ├── heatmap_binding_single_muts-1.png │ │ │ ├── heatmap_circulating_variants-1.png │ │ │ ├── permute_samples_0-1.png │ │ │ ├── permute_samples_0_expr-1.png │ │ │ ├── permute_samples_1-1.png │ │ │ ├── permute_samples_1_expr-1.png │ │ │ ├── permute_samples_5-1.png │ │ │ ├── permute_samples_5_expr-1.png │ │ │ ├── scatter_circulating_variants_ngeography-1.png │ │ │ └── scatter_circulating_variants_nobs-1.png │ ├── compute_binding_Kd.md │ ├── compute_binding_Kd_files │ │ └── figure-gfm │ │ │ ├── 1e-10_Kd-1.png │ │ │ ├── 1e-11_Kd-1.png │ │ │ ├── 1e-12_Kd-1.png │ │ │ ├── 1e-15_Kd-1.png │ │ │ ├── 1e-4_Kd-1.png │ │ │ ├── 1e-5_Kd-1.png │ │ │ ├── 1e-6_Kd-1.png │ │ │ ├── 1e-7_Kd-1.png │ │ │ ├── 1e-8_Kd-1.png │ │ │ ├── 1e-9_Kd-1.png │ │ │ ├── Kd_distribution-1.png │ │ │ ├── avgcount-1.png │ │ │ ├── censor_log10SE_max-1.png │ │ │ ├── check_failed_titrations-1.png │ │ │ ├── estimate_variance_lib1-1.png │ │ │ ├── estimate_variance_lib2-1.png │ │ │ ├── example_curves_cutoff_nMSR-1.png │ │ │ ├── example_curves_eliminated_nMSR-1.png │ │ │ ├── example_curves_median_nMSR-1.png │ │ │ ├── final_pheno_DFE-1.png │ │ │ ├── nMSR_distribution-1.png │ │ │ ├── spot_check_baseline-1.png │ │ │ └── spot_check_response-1.png │ ├── compute_expression_meanF.md │ ├── compute_expression_meanF_files │ │ └── figure-gfm │ │ │ ├── cell_count_coverage-1.png │ │ │ ├── estimate_variance-1.png │ │ │ ├── filtered_expression_distribution-1.png │ │ │ ├── unfiltered_expression_distribution-1.png │ │ │ └── violins_expression_distribution-1.png │ ├── count_variants.md │ ├── count_variants_files │ │ └── count_variants_38_0.png │ ├── dag.svg │ ├── global_epistasis_binding.md │ ├── global_epistasis_binding_files │ │ ├── global_epistasis_binding_24_0.png │ │ ├── global_epistasis_binding_24_1.png │ │ ├── global_epistasis_binding_24_2.png │ │ ├── global_epistasis_binding_27_0.png │ │ ├── global_epistasis_binding_27_1.png │ │ ├── global_epistasis_binding_27_2.png │ │ ├── global_epistasis_binding_33_0.png │ │ ├── global_epistasis_binding_33_1.png │ │ ├── global_epistasis_binding_33_2.png │ │ ├── global_epistasis_binding_35_0.png │ │ ├── global_epistasis_binding_35_1.png │ │ ├── global_epistasis_binding_35_2.png │ │ ├── global_epistasis_binding_41_0.png │ │ ├── global_epistasis_binding_41_1.png │ │ └── global_epistasis_binding_41_2.png │ ├── global_epistasis_expression.md │ ├── global_epistasis_expression_files │ │ ├── global_epistasis_expression_24_0.png │ │ ├── global_epistasis_expression_24_1.png │ │ ├── global_epistasis_expression_24_2.png │ │ ├── global_epistasis_expression_27_0.png │ │ ├── global_epistasis_expression_27_1.png │ │ ├── global_epistasis_expression_27_2.png │ │ ├── global_epistasis_expression_33_0.png │ │ ├── global_epistasis_expression_33_1.png │ │ └── global_epistasis_expression_33_2.png │ ├── interactive_heatmap.md │ ├── logoplots_of_muteffects.md │ ├── logoplots_of_muteffects_files │ │ ├── logoplots_of_muteffects_18_0.png │ │ ├── logoplots_of_muteffects_20_0.png │ │ ├── logoplots_of_muteffects_25_1.png │ │ ├── logoplots_of_muteffects_25_3.png │ │ ├── logoplots_of_muteffects_27_1.png │ │ ├── logoplots_of_muteffects_27_3.png │ │ ├── logoplots_of_muteffects_29_1.png │ │ ├── logoplots_of_muteffects_29_3.png │ │ ├── logoplots_of_muteffects_29_5.png │ │ ├── logoplots_of_muteffects_31_1.png │ │ ├── logoplots_of_muteffects_32_0.png │ │ ├── logoplots_of_muteffects_34_0.png │ │ └── logoplots_of_muteffects_36_0.png │ ├── process_ccs.md │ ├── process_ccs_files │ │ ├── process_ccs_17_1.png │ │ ├── process_ccs_25_0.png │ │ ├── process_ccs_27_0.png │ │ ├── process_ccs_27_1.png │ │ ├── process_ccs_27_2.png │ │ ├── process_ccs_35_0.png │ │ ├── process_ccs_37_0.png │ │ ├── process_ccs_39_0.png │ │ ├── process_ccs_41_0.png │ │ ├── process_ccs_45_0.png │ │ └── process_ccs_47_0.png │ ├── sarbecovirus_diversity.md │ ├── sarbecovirus_diversity_files │ │ └── figure-gfm │ │ │ ├── heatmap_SARS_CoV_2_1_diff-1.png │ │ │ ├── heatmap_SARS_CoV_2_BM4831_diff-1.png │ │ │ ├── heatmap_SARS_CoV_2_GDPangolin_diff-1.png │ │ │ ├── heatmap_SARS_CoV_2_HKU31_diff-1.png │ │ │ ├── heatmap_SARS_CoV_2_RaTG13_diff-1.png │ │ │ ├── homolog_amino_acid_variants-1.png │ │ │ ├── natural_diversity_v_mean_effects-1.png │ │ │ ├── predicted_versus_actual_homolog_correlations_RBD-1.png │ │ │ └── predicted_versus_actual_homolog_correlations_RBM-1.png │ ├── single_mut_effects.md │ ├── single_mut_effects_files │ │ └── figure-gfm │ │ │ ├── bc_tables-1.png │ │ │ ├── betas_bind_lib1_v_lib2-1.png │ │ │ ├── betas_expr_lib1_v_lib2-1.png │ │ │ ├── betas_expr_lib1_v_lib2_filtered-1.png │ │ │ ├── bind_avg_coefs_v_direct_singles-1.png │ │ │ ├── bind_coef_no_direct-1.png │ │ │ ├── bind_effects_direct_singles-1.png │ │ │ ├── bind_effects_direct_singles_plot-1.png │ │ │ ├── bind_final_correlation-1.png │ │ │ ├── bind_lib1_coef_v_lib2_direct-1.png │ │ │ ├── expr_avg_coefs_v_direct_singles-1.png │ │ │ ├── expr_effects_direct_singles-1.png │ │ │ ├── expr_effects_direct_singles_plot-1.png │ │ │ ├── expr_final_correlation-1.png │ │ │ ├── homolog_isogenic_validations-1.png │ │ │ ├── homologs_DMS_v_functional_pvirus_entry-1.png │ │ │ ├── homologs_isogenic_v_functional_pvirus_entry-1.png │ │ │ ├── homologs_lib1_lib2_correlation-1.png │ │ │ ├── response_v_expression-1.png │ │ │ └── single_mut_isogenic_validations-1.png │ ├── structure_function.md │ ├── structure_function_files │ │ └── figure-gfm │ │ │ ├── DFE_bind-1.png │ │ │ ├── DFE_ridgeplots-1.png │ │ │ ├── RBM_versus_core_fold_mutations-1.png │ │ │ ├── correlation_mut_expression_binding-1.png │ │ │ ├── heatmap_ACE2_contacts-1.png │ │ │ ├── heatmap_bind_expr_NLGS-1.png │ │ │ ├── heatmap_bind_expr_disulfide-1.png │ │ │ ├── heatmap_binding_all_sites-1.png │ │ │ ├── heatmap_expression_all-1.png │ │ │ ├── heatmap_homolog_phenotypes-1.png │ │ │ ├── heatmap_stability_binding_tradeoffs-1.png │ │ │ ├── mean_mut_effect_versus_RSA-1.png │ │ │ ├── n_NLGS_phenotype_corr-1.png │ │ │ ├── pairwise_deviations_plots-1.png │ │ │ ├── plot_epistasis_v_residue_pair_distance-1.png │ │ │ ├── plot_epistasis_v_residue_pair_distance_RBM-1.png │ │ │ └── stripplot_ACE2_contacts_homologs-1.png │ └── summary.md └── variants │ └── codon_variant_table.csv ├── run_Hutch_cluster.bash ├── sarbecovirus_diversity.Rmd ├── scripts └── run_nb.py ├── single_mut_effects.Rmd ├── structural_views ├── README.md ├── color_spheres_by_constraint.txt ├── images_epitope-outlines │ ├── 80R_view1_overlay.png │ ├── 80R_view2_overlay.png │ ├── ACE2_view1_overlay.png │ ├── ACE2_view2_overlay.png │ ├── B38_view1_overlay.png │ ├── B38_view2_overlay.png │ ├── CR3022_view2_overlay.png │ ├── F26G19_view2_overlay.png │ ├── RBD_bind_view1.png │ ├── RBD_bind_view2.png │ ├── RBD_bind_view3.png │ ├── RBD_bind_view3_NLGS.png │ ├── RBD_expr_view1.png │ ├── RBD_expr_view2.png │ ├── RBD_expr_view3.png │ ├── RBD_expr_view3_NLGS.png │ ├── S230_view2_overlay.png │ ├── S309_view3_NLGS_overlay.png │ ├── S309_view3_overlay.png │ ├── VHH72_view2_overlay.png │ ├── hypothetical-epitope_view3_overlay.png │ └── m396_view2_overlay.png ├── images_epitope_commands.txt ├── images_global-sensitivity │ ├── G502_steric_contraint.png │ ├── RBD_bind-specific-constraint.png │ ├── RBD_bind_view1.png │ ├── RBD_expr_view1.png │ ├── RBD_new-NLGS.png │ ├── example_interface_contacts.png │ └── interface-hydrophobic_packing_constraint.png ├── surface_constraint_commands.txt └── surface_constraint_features.pse └── structure_function.Rmd /.gitattributes: -------------------------------------------------------------------------------- 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