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<h1 id="deep-mutational-scanning-of-the-sars-cov-2-xbb15-rbd-using-a-barcoded-lentiviral-platform">Deep mutational scanning of the SARS-CoV-2 XBB.1.5 RBD using a barcoded lentiviral platform</h1>
<p>Analysis by <a href="https://doi.org/10.1101/2023.11.13.566961">Dadonaite et al, bioRxiv, DOI 10.1101/2023.11.13.566961</a> (2023)</p>
<p>See <a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS">https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS</a> for full code.</p>
<div class="toc"><span class="toctitle">Contents</span><ul>
<li><a href="#barcode-to-codon-variant-lookup-table">Barcode to codon-variant lookup table</a></li>
<li><a href="#count-barcodes-for-variants">Count barcodes for variants</a></li>
<li><a href="#functional-effects-of-mutations">Functional effects of mutations</a></li>
<li><a href="#antibodyserum-escape">Antibody/serum escape</a></li>
<li><a href="#ace2-binding">ACE2 binding</a></li>
<li><a href="#summary-of-results-across-assays">Summary of results across assays</a></li>
<li><a href="#additional-data-files">Additional data files</a></li>
</ul>
</div>
<h2 id="barcode-to-codon-variant-lookup-table">Barcode to codon-variant lookup table</h2>
<h4 id="analysis-notebooks">Analysis notebooks</h4>
<ul>
<li><a href="notebooks/analyze_pacbio_ccs.html">Analysis of PacBio CCSs</a></li>
<li><a href="notebooks/build_pacbio_consensus.html">Building barcoded variant consensus sequences</a></li>
<li><a href="notebooks/build_codon_variants.html">Building of codon-variant table</a></li>
</ul>
<h4 id="data-files">Data files</h4>
<ul>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/gene_sequence/codon.fasta">parental codon sequence</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/gene_sequence/protein.fasta">parental protein sequence</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/variants/codon_variants.csv">barcode to codon-variant lookup table</a></li>
</ul>
<h2 id="count-barcodes-for-variants">Count barcodes for variants</h2>
<h4 id="analysis-notebooks_1">Analysis notebooks</h4>
<ul>
<li><a href="notebooks/analyze_variant_counts.html">Analysis of variant counts</a></li>
</ul>
<h4 id="data-files_1">Data files</h4>
<ul>
<li><details><summary>Barcode count CSVs (click triangle to expand/collapse)</summary><ul>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230614-VSVG-control_counts.csv">Lib1-230614-VSVG-control</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230614-VSVG-control_counts.csv">Lib2-230614-VSVG-control</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230614-no-antibody-control_counts.csv">Lib1-230614-no-antibody-control</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230614-no-antibody-control_counts.csv">Lib2-230614-no-antibody-control</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230615-no-antibody-control-medium-ACE2_counts.csv">Lib1-230615-no-antibody-control-medium-ACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230615-no-antibody-control-medium-ACE2_counts.csv">Lib2-230615-no-antibody-control-medium-ACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230615-antibody-monomeric-ACE2-2.88_counts.csv">Lib1-230615-antibody-monomeric-ACE2-2.88</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230615-antibody-monomeric-ACE2-8.633016_counts.csv">Lib1-230615-antibody-monomeric-ACE2-8.633016</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230615-antibody-monomeric-ACE2-25.899048_counts.csv">Lib1-230615-antibody-monomeric-ACE2-25.899048</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230615-antibody-monomeric-ACE2-77.697144_counts.csv">Lib1-230615-antibody-monomeric-ACE2-77.697144</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230615-antibody-monomeric-ACE2-233.091432_counts.csv">Lib1-230615-antibody-monomeric-ACE2-233.091432</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230615-antibody-monomeric-ACE2-2.88_counts.csv">Lib2-230615-antibody-monomeric-ACE2-2.88</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230615-antibody-monomeric-ACE2-8.633016_counts.csv">Lib2-230615-antibody-monomeric-ACE2-8.633016</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230615-antibody-monomeric-ACE2-25.899048_counts.csv">Lib2-230615-antibody-monomeric-ACE2-25.899048</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230615-antibody-monomeric-ACE2-77.697144_counts.csv">Lib2-230615-antibody-monomeric-ACE2-77.697144</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230615-antibody-monomeric-ACE2-233.091432_counts.csv">Lib2-230615-antibody-monomeric-ACE2-233.091432</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230613-no-antibody-control_counts.csv">Lib1-230613-no-antibody-control</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230613-antibody-dimeric-ACE2-0.21_counts.csv">Lib1-230613-antibody-dimeric-ACE2-0.21</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230613-antibody-dimeric-ACE2-0.63_counts.csv">Lib1-230613-antibody-dimeric-ACE2-0.63</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230613-antibody-dimeric-ACE2-1.89_counts.csv">Lib1-230613-antibody-dimeric-ACE2-1.89</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230613-antibody-dimeric-ACE2-5.67_counts.csv">Lib1-230613-antibody-dimeric-ACE2-5.67</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230613-antibody-dimeric-ACE2-17.01_counts.csv">Lib1-230613-antibody-dimeric-ACE2-17.01</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230613-no-antibody-control_counts.csv">Lib2-230613-no-antibody-control</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230613-antibody-dimeric-ACE2-0.21_counts.csv">Lib2-230613-antibody-dimeric-ACE2-0.21</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230613-antibody-dimeric-ACE2-0.63_counts.csv">Lib2-230613-antibody-dimeric-ACE2-0.63</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230613-antibody-dimeric-ACE2-1.89_counts.csv">Lib2-230613-antibody-dimeric-ACE2-1.89</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230613-antibody-dimeric-ACE2-5.67_counts.csv">Lib2-230613-antibody-dimeric-ACE2-5.67</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230613-antibody-dimeric-ACE2-17.01_counts.csv">Lib2-230613-antibody-dimeric-ACE2-17.01</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-343C_0.013_mediumACE2_counts.csv">Lib1-230815-sera-343C_0.013_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-343C_0.052_mediumACE2_counts.csv">Lib1-230815-sera-343C_0.052_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-343C_0.152_mediumACE2_counts.csv">Lib1-230815-sera-343C_0.152_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-493C_0.045_mediumACE2_counts.csv">Lib1-230815-sera-493C_0.045_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-493C_0.091_mediumACE2_counts.csv">Lib1-230815-sera-493C_0.091_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-493C_0.16_mediumACE2_counts.csv">Lib1-230815-sera-493C_0.16_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-498C_0.015_mediumACE2_counts.csv">Lib1-230815-sera-498C_0.015_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-498C_0.058_mediumACE2_counts.csv">Lib1-230815-sera-498C_0.058_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-498C_0.197_mediumACE2_counts.csv">Lib1-230815-sera-498C_0.197_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-500C_0.01_mediumACE2_counts.csv">Lib1-230815-sera-500C_0.01_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-500C_0.043_mediumACE2_counts.csv">Lib1-230815-sera-500C_0.043_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-500C_0.099_mediumACE2_counts.csv">Lib1-230815-sera-500C_0.099_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-503C_0.065_mediumACE2_counts.csv">Lib1-230815-sera-503C_0.065_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-503C_0.091_mediumACE2_counts.csv">Lib1-230815-sera-503C_0.091_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-503C_0.136_mediumACE2_counts.csv">Lib1-230815-sera-503C_0.136_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib1-230815-no-antibody_control_mediumACE2_counts.csv">Lib1-230815-no-antibody_control_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-343C_0.013_mediumACE2_counts.csv">Lib2-230815-sera-343C_0.013_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-343C_0.052_mediumACE2_counts.csv">Lib2-230815-sera-343C_0.052_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-343C_0.152_mediumACE2_counts.csv">Lib2-230815-sera-343C_0.152_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-493C_0.045_mediumACE2_counts.csv">Lib2-230815-sera-493C_0.045_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-493C_0.091_mediumACE2_counts.csv">Lib2-230815-sera-493C_0.091_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-493C_0.16_mediumACE2_counts.csv">Lib2-230815-sera-493C_0.16_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-498C_0.015_mediumACE2_counts.csv">Lib2-230815-sera-498C_0.015_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-498C_0.058_mediumACE2_counts.csv">Lib2-230815-sera-498C_0.058_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-498C_0.197_mediumACE2_counts.csv">Lib2-230815-sera-498C_0.197_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-500C_0.01_mediumACE2_counts.csv">Lib2-230815-sera-500C_0.01_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-500C_0.043_mediumACE2_counts.csv">Lib2-230815-sera-500C_0.043_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-500C_0.099_mediumACE2_counts.csv">Lib2-230815-sera-500C_0.099_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-503C_0.065_mediumACE2_counts.csv">Lib2-230815-sera-503C_0.065_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-503C_0.091_mediumACE2_counts.csv">Lib2-230815-sera-503C_0.091_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-503C_0.136_mediumACE2_counts.csv">Lib2-230815-sera-503C_0.136_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/barcode_counts/Lib2-230815-no-antibody_control_mediumACE2_counts.csv">Lib2-230815-no-antibody_control_mediumACE2</a></li>
</ul></details>
</li>
</ul>
<h2 id="functional-effects-of-mutations">Functional effects of mutations</h2>
<h4 id="final-summary-plots">Final summary plots</h4>
<ul>
<li><details><summary>Interactive plots of average mutation functional effects (click triangle to expand/collapse)</summary><ul>
<li><a href="htmls/293T_high_ACE2_entry_func_effects.html">293T_high_ACE2_entry</a></li>
</ul></details>
</li>
<li><details><summary>Interactive plots of average mutation latent-phenotype effects (click triangle to expand/collapse)</summary><ul>
<li><a href="htmls/293T_high_ACE2_entry_latent_effects.html">293T_high_ACE2_entry</a></li>
</ul></details>
</li>
</ul>
<h4 id="analysis-notebooks_2">Analysis notebooks</h4>
<ul>
<li><a href="notebooks/analyze_func_scores.html">Analysis of functional scores</a></li>
<li><details><summary>Notebooks with per-selection global epistasis fitting (click triangle to expand/collapse)</summary><ul>
<li><a href="notebooks/func_effects_global_epistasis_Lib1-230614-293T-ACE2-1.html">Lib1-230614-293T-ACE2-1</a></li>
<li><a href="notebooks/func_effects_global_epistasis_Lib2-230614-293T-ACE2-1.html">Lib2-230614-293T-ACE2-1</a></li>
</ul></details>
</li>
<li><details><summary>Notebooks averaging mutation functional effects (click triangle to expand/collapse)</summary><ul>
<li><a href="notebooks/avg_func_effects_293T_high_ACE2_entry.html">293T_high_ACE2_entry</a></li>
</ul></details>
</li>
</ul>
<h4 id="data-files_2">Data files</h4>
<ul>
<li><details><summary>Per-variant functional score CSVs (click triangle to expand/collapse)</summary><ul>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/func_scores/Lib1-230614-293T-ACE2-1_func_scores.csv">Lib1-230614-293T-ACE2-1</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/func_scores/Lib2-230614-293T-ACE2-1_func_scores.csv">Lib2-230614-293T-ACE2-1</a></li>
</ul></details>
</li>
<li><details><summary>Per-selection mutation functional effect CSVs (click triangle to expand/collapse)</summary><ul>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/func_effects/by_selection/Lib1-230614-293T-ACE2-1_func_effects.csv">Lib1-230614-293T-ACE2-1</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/func_effects/by_selection/Lib2-230614-293T-ACE2-1_func_effects.csv">Lib2-230614-293T-ACE2-1</a></li>
</ul></details>
</li>
<li><details><summary>Average mutation functional effects (CSV files) (click triangle to expand/collapse)</summary><ul>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/func_effects/averages/293T_high_ACE2_entry_func_effects.csv">293T_high_ACE2_entry</a></li>
</ul></details>
</li>
<li><details><summary>Average mutation latent-phenotype effects (CSV files) (click triangle to expand/collapse)</summary><ul>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/func_effects/averages/293T_high_ACE2_entry_func_effects.csv">293T_high_ACE2_entry</a></li>
</ul></details>
</li>
</ul>
<h2 id="antibodyserum-escape">Antibody/serum escape</h2>
<h4 id="final-summary-plots_1">Final summary plots</h4>
<ul>
<li><details><summary>antibody escape mutation effect plots (click triangle to expand/collapse)</summary><ul>
<li><a href="htmls/sera_493C_mediumACE2_mut_effect.html">sera_493C_mediumACE2</a></li>
<li><a href="htmls/sera_498C_mediumACE2_mut_effect.html">sera_498C_mediumACE2</a></li>
<li><a href="htmls/sera_500C_mediumACE2_mut_effect.html">sera_500C_mediumACE2</a></li>
<li><a href="htmls/sera_503C_mediumACE2_mut_effect.html">sera_503C_mediumACE2</a></li>
<li><a href="htmls/sera_343C_mediumACE2_mut_effect.html">sera_343C_mediumACE2</a></li>
</ul></details>
</li>
</ul>
<h4 id="analysis-notebooks_3">Analysis notebooks</h4>
<ul>
<li><details><summary>Fits of polyclonal models to individual antibody escape selections (click triangle to expand/collapse)</summary><ul>
<li><a href="notebooks/fit_escape_antibody_escape_Lib1-230815-sera-343C_mediumACE2.html">Lib1-230815-sera-343C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib2-230815-sera-343C_mediumACE2.html">Lib2-230815-sera-343C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib1-230815-sera-493C_mediumACE2.html">Lib1-230815-sera-493C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib2-230815-sera-493C_mediumACE2.html">Lib2-230815-sera-493C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib1-230815-sera-498C_mediumACE2.html">Lib1-230815-sera-498C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib2-230815-sera-498C_mediumACE2.html">Lib2-230815-sera-498C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib1-230815-sera-500C_mediumACE2.html">Lib1-230815-sera-500C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib2-230815-sera-500C_mediumACE2.html">Lib2-230815-sera-500C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib1-230815-sera-503C_mediumACE2.html">Lib1-230815-sera-503C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib2-230815-sera-503C_mediumACE2.html">Lib2-230815-sera-503C_mediumACE2</a></li>
</ul></details>
</li>
<li><details><summary>Average selections for antibody escape (click triangle to expand/collapse)</summary><ul>
<li><a href="notebooks/avg_escape_antibody_escape_sera_493C_mediumACE2.html">sera_493C_mediumACE2</a></li>
<li><a href="notebooks/avg_escape_antibody_escape_sera_498C_mediumACE2.html">sera_498C_mediumACE2</a></li>
<li><a href="notebooks/avg_escape_antibody_escape_sera_500C_mediumACE2.html">sera_500C_mediumACE2</a></li>
<li><a href="notebooks/avg_escape_antibody_escape_sera_503C_mediumACE2.html">sera_503C_mediumACE2</a></li>
<li><a href="notebooks/avg_escape_antibody_escape_sera_343C_mediumACE2.html">sera_343C_mediumACE2</a></li>
</ul></details>
</li>
</ul>
<h4 id="data-files_3">Data files</h4>
<ul>
<li><details><summary>Probability (fraction) escape for each variant in each antibody escape selection (CSVs) (click triangle to expand/collapse)</summary><ul>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-343C_mediumACE2/Lib1-230815-sera-343C_0.013_mediumACE2_prob_escape.csv">Lib1-230815-sera-343C_mediumACE2 Lib1-230815-sera-343C_0.013_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-343C_mediumACE2/Lib1-230815-sera-343C_0.052_mediumACE2_prob_escape.csv">Lib1-230815-sera-343C_mediumACE2 Lib1-230815-sera-343C_0.052_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-343C_mediumACE2/Lib1-230815-sera-343C_0.152_mediumACE2_prob_escape.csv">Lib1-230815-sera-343C_mediumACE2 Lib1-230815-sera-343C_0.152_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-343C_mediumACE2/Lib2-230815-sera-343C_0.013_mediumACE2_prob_escape.csv">Lib2-230815-sera-343C_mediumACE2 Lib2-230815-sera-343C_0.013_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-343C_mediumACE2/Lib2-230815-sera-343C_0.052_mediumACE2_prob_escape.csv">Lib2-230815-sera-343C_mediumACE2 Lib2-230815-sera-343C_0.052_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-343C_mediumACE2/Lib2-230815-sera-343C_0.152_mediumACE2_prob_escape.csv">Lib2-230815-sera-343C_mediumACE2 Lib2-230815-sera-343C_0.152_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-493C_mediumACE2/Lib1-230815-sera-493C_0.045_mediumACE2_prob_escape.csv">Lib1-230815-sera-493C_mediumACE2 Lib1-230815-sera-493C_0.045_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-493C_mediumACE2/Lib1-230815-sera-493C_0.091_mediumACE2_prob_escape.csv">Lib1-230815-sera-493C_mediumACE2 Lib1-230815-sera-493C_0.091_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-493C_mediumACE2/Lib1-230815-sera-493C_0.16_mediumACE2_prob_escape.csv">Lib1-230815-sera-493C_mediumACE2 Lib1-230815-sera-493C_0.16_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-493C_mediumACE2/Lib2-230815-sera-493C_0.045_mediumACE2_prob_escape.csv">Lib2-230815-sera-493C_mediumACE2 Lib2-230815-sera-493C_0.045_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-493C_mediumACE2/Lib2-230815-sera-493C_0.091_mediumACE2_prob_escape.csv">Lib2-230815-sera-493C_mediumACE2 Lib2-230815-sera-493C_0.091_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-493C_mediumACE2/Lib2-230815-sera-493C_0.16_mediumACE2_prob_escape.csv">Lib2-230815-sera-493C_mediumACE2 Lib2-230815-sera-493C_0.16_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-498C_mediumACE2/Lib1-230815-sera-498C_0.015_mediumACE2_prob_escape.csv">Lib1-230815-sera-498C_mediumACE2 Lib1-230815-sera-498C_0.015_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-498C_mediumACE2/Lib1-230815-sera-498C_0.058_mediumACE2_prob_escape.csv">Lib1-230815-sera-498C_mediumACE2 Lib1-230815-sera-498C_0.058_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-498C_mediumACE2/Lib1-230815-sera-498C_0.197_mediumACE2_prob_escape.csv">Lib1-230815-sera-498C_mediumACE2 Lib1-230815-sera-498C_0.197_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-498C_mediumACE2/Lib2-230815-sera-498C_0.015_mediumACE2_prob_escape.csv">Lib2-230815-sera-498C_mediumACE2 Lib2-230815-sera-498C_0.015_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-498C_mediumACE2/Lib2-230815-sera-498C_0.058_mediumACE2_prob_escape.csv">Lib2-230815-sera-498C_mediumACE2 Lib2-230815-sera-498C_0.058_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-498C_mediumACE2/Lib2-230815-sera-498C_0.197_mediumACE2_prob_escape.csv">Lib2-230815-sera-498C_mediumACE2 Lib2-230815-sera-498C_0.197_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-500C_mediumACE2/Lib1-230815-sera-500C_0.01_mediumACE2_prob_escape.csv">Lib1-230815-sera-500C_mediumACE2 Lib1-230815-sera-500C_0.01_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-500C_mediumACE2/Lib1-230815-sera-500C_0.043_mediumACE2_prob_escape.csv">Lib1-230815-sera-500C_mediumACE2 Lib1-230815-sera-500C_0.043_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-500C_mediumACE2/Lib1-230815-sera-500C_0.099_mediumACE2_prob_escape.csv">Lib1-230815-sera-500C_mediumACE2 Lib1-230815-sera-500C_0.099_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-500C_mediumACE2/Lib2-230815-sera-500C_0.01_mediumACE2_prob_escape.csv">Lib2-230815-sera-500C_mediumACE2 Lib2-230815-sera-500C_0.01_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-500C_mediumACE2/Lib2-230815-sera-500C_0.043_mediumACE2_prob_escape.csv">Lib2-230815-sera-500C_mediumACE2 Lib2-230815-sera-500C_0.043_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-500C_mediumACE2/Lib2-230815-sera-500C_0.099_mediumACE2_prob_escape.csv">Lib2-230815-sera-500C_mediumACE2 Lib2-230815-sera-500C_0.099_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-503C_mediumACE2/Lib1-230815-sera-503C_0.065_mediumACE2_prob_escape.csv">Lib1-230815-sera-503C_mediumACE2 Lib1-230815-sera-503C_0.065_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-503C_mediumACE2/Lib1-230815-sera-503C_0.091_mediumACE2_prob_escape.csv">Lib1-230815-sera-503C_mediumACE2 Lib1-230815-sera-503C_0.091_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-503C_mediumACE2/Lib1-230815-sera-503C_0.136_mediumACE2_prob_escape.csv">Lib1-230815-sera-503C_mediumACE2 Lib1-230815-sera-503C_0.136_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-503C_mediumACE2/Lib2-230815-sera-503C_0.065_mediumACE2_prob_escape.csv">Lib2-230815-sera-503C_mediumACE2 Lib2-230815-sera-503C_0.065_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-503C_mediumACE2/Lib2-230815-sera-503C_0.091_mediumACE2_prob_escape.csv">Lib2-230815-sera-503C_mediumACE2 Lib2-230815-sera-503C_0.091_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-503C_mediumACE2/Lib2-230815-sera-503C_0.136_mediumACE2_prob_escape.csv">Lib2-230815-sera-503C_mediumACE2 Lib2-230815-sera-503C_0.136_mediumACE2</a></li>
</ul></details>
</li>
<li><details><summary>antibody escape CSVs (click triangle to expand/collapse)</summary><ul>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/averages/sera_493C_mediumACE2_mut_effect.csv">sera_493C_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/averages/sera_498C_mediumACE2_mut_effect.csv">sera_498C_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/averages/sera_500C_mediumACE2_mut_effect.csv">sera_500C_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/averages/sera_503C_mediumACE2_mut_effect.csv">sera_503C_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/antibody_escape/averages/sera_343C_mediumACE2_mut_effect.csv">sera_343C_mediumACE2</a></li>
</ul></details>
</li>
</ul>
<h2 id="ace2-binding">ACE2 binding</h2>
<h4 id="final-summary-plots_2">Final summary plots</h4>
<ul>
<li><details><summary>ACE2 binding mutation effect plots (click triangle to expand/collapse)</summary><ul>
<li><a href="htmls/monomeric_ACE2_mut_effect.html">monomeric_ACE2</a></li>
<li><a href="htmls/dimeric_ACE2_mut_effect.html">dimeric_ACE2</a></li>
</ul></details>
</li>
</ul>
<h4 id="analysis-notebooks_4">Analysis notebooks</h4>
<ul>
<li><details><summary>Fits of polyclonal models to individual ACE2 binding selections (click triangle to expand/collapse)</summary><ul>
<li><a href="notebooks/fit_escape_ACE2_binding_Lib1-230615-monomeric-ACE2.html">Lib1-230615-monomeric-ACE2</a></li>
<li><a href="notebooks/fit_escape_ACE2_binding_Lib2-230615-monomeric-ACE2.html">Lib2-230615-monomeric-ACE2</a></li>
<li><a href="notebooks/fit_escape_ACE2_binding_Lib1-230613-dimeric-ACE2.html">Lib1-230613-dimeric-ACE2</a></li>
<li><a href="notebooks/fit_escape_ACE2_binding_Lib2-230613-dimeric-ACE2.html">Lib2-230613-dimeric-ACE2</a></li>
</ul></details>
</li>
<li><details><summary>Average selections for ACE2 binding (click triangle to expand/collapse)</summary><ul>
<li><a href="notebooks/avg_escape_ACE2_binding_monomeric_ACE2.html">monomeric_ACE2</a></li>
<li><a href="notebooks/avg_escape_ACE2_binding_dimeric_ACE2.html">dimeric_ACE2</a></li>
</ul></details>
</li>
</ul>
<h4 id="data-files_4">Data files</h4>
<ul>
<li><details><summary>Probability (fraction) escape for each variant in each ACE2 binding selection (CSVs) (click triangle to expand/collapse)</summary><ul>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/by_selection/Lib1-230615-monomeric-ACE2/Lib1-230615-antibody-monomeric-ACE2-2.88_prob_escape.csv">Lib1-230615-monomeric-ACE2 Lib1-230615-antibody-monomeric-ACE2-2.88</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/by_selection/Lib1-230615-monomeric-ACE2/Lib1-230615-antibody-monomeric-ACE2-8.633016_prob_escape.csv">Lib1-230615-monomeric-ACE2 Lib1-230615-antibody-monomeric-ACE2-8.633016</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/by_selection/Lib1-230615-monomeric-ACE2/Lib1-230615-antibody-monomeric-ACE2-25.899048_prob_escape.csv">Lib1-230615-monomeric-ACE2 Lib1-230615-antibody-monomeric-ACE2-25.899048</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/by_selection/Lib1-230615-monomeric-ACE2/Lib1-230615-antibody-monomeric-ACE2-77.697144_prob_escape.csv">Lib1-230615-monomeric-ACE2 Lib1-230615-antibody-monomeric-ACE2-77.697144</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/by_selection/Lib1-230615-monomeric-ACE2/Lib1-230615-antibody-monomeric-ACE2-233.091432_prob_escape.csv">Lib1-230615-monomeric-ACE2 Lib1-230615-antibody-monomeric-ACE2-233.091432</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/by_selection/Lib2-230615-monomeric-ACE2/Lib2-230615-antibody-monomeric-ACE2-2.88_prob_escape.csv">Lib2-230615-monomeric-ACE2 Lib2-230615-antibody-monomeric-ACE2-2.88</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/by_selection/Lib2-230615-monomeric-ACE2/Lib2-230615-antibody-monomeric-ACE2-8.633016_prob_escape.csv">Lib2-230615-monomeric-ACE2 Lib2-230615-antibody-monomeric-ACE2-8.633016</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/by_selection/Lib2-230615-monomeric-ACE2/Lib2-230615-antibody-monomeric-ACE2-25.899048_prob_escape.csv">Lib2-230615-monomeric-ACE2 Lib2-230615-antibody-monomeric-ACE2-25.899048</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/by_selection/Lib2-230615-monomeric-ACE2/Lib2-230615-antibody-monomeric-ACE2-77.697144_prob_escape.csv">Lib2-230615-monomeric-ACE2 Lib2-230615-antibody-monomeric-ACE2-77.697144</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/by_selection/Lib2-230615-monomeric-ACE2/Lib2-230615-antibody-monomeric-ACE2-233.091432_prob_escape.csv">Lib2-230615-monomeric-ACE2 Lib2-230615-antibody-monomeric-ACE2-233.091432</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/by_selection/Lib1-230613-dimeric-ACE2/Lib1-230613-antibody-dimeric-ACE2-0.21_prob_escape.csv">Lib1-230613-dimeric-ACE2 Lib1-230613-antibody-dimeric-ACE2-0.21</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/by_selection/Lib1-230613-dimeric-ACE2/Lib1-230613-antibody-dimeric-ACE2-0.63_prob_escape.csv">Lib1-230613-dimeric-ACE2 Lib1-230613-antibody-dimeric-ACE2-0.63</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/by_selection/Lib1-230613-dimeric-ACE2/Lib1-230613-antibody-dimeric-ACE2-1.89_prob_escape.csv">Lib1-230613-dimeric-ACE2 Lib1-230613-antibody-dimeric-ACE2-1.89</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/by_selection/Lib1-230613-dimeric-ACE2/Lib1-230613-antibody-dimeric-ACE2-5.67_prob_escape.csv">Lib1-230613-dimeric-ACE2 Lib1-230613-antibody-dimeric-ACE2-5.67</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/by_selection/Lib1-230613-dimeric-ACE2/Lib1-230613-antibody-dimeric-ACE2-17.01_prob_escape.csv">Lib1-230613-dimeric-ACE2 Lib1-230613-antibody-dimeric-ACE2-17.01</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/by_selection/Lib2-230613-dimeric-ACE2/Lib2-230613-antibody-dimeric-ACE2-0.21_prob_escape.csv">Lib2-230613-dimeric-ACE2 Lib2-230613-antibody-dimeric-ACE2-0.21</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/by_selection/Lib2-230613-dimeric-ACE2/Lib2-230613-antibody-dimeric-ACE2-0.63_prob_escape.csv">Lib2-230613-dimeric-ACE2 Lib2-230613-antibody-dimeric-ACE2-0.63</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/by_selection/Lib2-230613-dimeric-ACE2/Lib2-230613-antibody-dimeric-ACE2-1.89_prob_escape.csv">Lib2-230613-dimeric-ACE2 Lib2-230613-antibody-dimeric-ACE2-1.89</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/by_selection/Lib2-230613-dimeric-ACE2/Lib2-230613-antibody-dimeric-ACE2-5.67_prob_escape.csv">Lib2-230613-dimeric-ACE2 Lib2-230613-antibody-dimeric-ACE2-5.67</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/by_selection/Lib2-230613-dimeric-ACE2/Lib2-230613-antibody-dimeric-ACE2-17.01_prob_escape.csv">Lib2-230613-dimeric-ACE2 Lib2-230613-antibody-dimeric-ACE2-17.01</a></li>
</ul></details>
</li>
<li><details><summary>ACE2 binding CSVs (click triangle to expand/collapse)</summary><ul>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/averages/monomeric_ACE2_mut_effect.csv">monomeric_ACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/ACE2_binding/averages/dimeric_ACE2_mut_effect.csv">dimeric_ACE2</a></li>
</ul></details>
</li>
</ul>
<h2 id="summary-of-results-across-assays">Summary of results across assays</h2>
<h4 id="final-summary-plots_3">Final summary plots</h4>
<ul>
<li><a href="htmls/summary_overlaid.html">Summary of assays (escape overlaid)</a></li>
<li><a href="htmls/summary_faceted.html">Summary of assays (escape faceted)</a></li>
</ul>
<h4 id="data-files_5">Data files</h4>
<ul>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/results/summaries/summary.csv">CSV summarizing results</a></li>
</ul>
<h2 id="additional-data-files">Additional data files</h2>
<h4 id="spike-site-numbering">Spike site numbering</h4>
<ul>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_RBD_DMS/blob/main/data/site_numbering_map.csv">CSV converting sequential sites in XBB.1.5 spike to Wuhan-Hu-1 reference sites</a></li>
</ul>