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<h1 id="deep-mutational-scanning-of-sars-cov-2-xbb15-spike-using-a-barcoded-lentiviral-platform">Deep mutational scanning of SARS-CoV-2 XBB.1.5 spike using a barcoded lentiviral platform</h1>
<p>Analysis by <a href="https://www.nature.com/articles/s41586-024-07636-1">Dadonaite et al, Nature (2024)</a> (2023)</p>
<p>See <a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS">https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_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-files-and-charts">Additional files and charts</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_spike_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_spike_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_spike_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_spike_DMS/blob/main/results/barcode_counts/Lib1-230614-VSVG_control_293T_counts.csv">Lib1-230614-VSVG_control_293T</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230614-VSVG_control_293T_counts.csv">Lib2-230614-VSVG_control_293T</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230614-no-antibody_control_highACE2_counts.csv">Lib1-230614-no-antibody_control_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230614-no-antibody_control_highACE2_counts.csv">Lib2-230614-no-antibody_control_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230614-no-antibody_control_mediumACE2_counts.csv">Lib1-230614-no-antibody_control_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230614-no-antibody_control_mediumACE2_counts.csv">Lib2-230614-no-antibody_control_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230729-no-antibody_control_highACE2_counts.csv">Lib1-230729-no-antibody_control_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230729-sera-503C_0.008483_highACE2_counts.csv">Lib1-230729-sera-503C_0.008483_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230729-sera-503C_0.033932_highACE2_counts.csv">Lib1-230729-sera-503C_0.033932_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230729-sera-503C_0.135728_highACE2_counts.csv">Lib1-230729-sera-503C_0.135728_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230720-sera-493C_0.045_highACE2_counts.csv">Lib1-230720-sera-493C_0.045_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230720-sera-493C_0.091_highACE2_counts.csv">Lib1-230720-sera-493C_0.091_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230720-sera-493C_0.16_highACE2_counts.csv">Lib1-230720-sera-493C_0.16_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230720-sera-493C_0.045_highACE2_counts.csv">Lib2-230720-sera-493C_0.045_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230720-sera-493C_0.091_highACE2_counts.csv">Lib2-230720-sera-493C_0.091_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230720-sera-493C_0.16_highACE2_counts.csv">Lib2-230720-sera-493C_0.16_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230720-sera-498C_0.015_highACE2_counts.csv">Lib1-230720-sera-498C_0.015_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230720-sera-498C_0.058_highACE2_counts.csv">Lib1-230720-sera-498C_0.058_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230720-sera-498C_0.197_highACE2_counts.csv">Lib1-230720-sera-498C_0.197_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230720-sera-498C_0.015_highACE2_counts.csv">Lib2-230720-sera-498C_0.015_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230720-sera-498C_0.058_highACE2_counts.csv">Lib2-230720-sera-498C_0.058_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230720-sera-498C_0.197_highACE2_counts.csv">Lib2-230720-sera-498C_0.197_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230720-sera-500C_0.01_highACE2_counts.csv">Lib1-230720-sera-500C_0.01_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230720-sera-500C_0.043_highACE2_counts.csv">Lib1-230720-sera-500C_0.043_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230720-sera-500C_0.111_highACE2_counts.csv">Lib1-230720-sera-500C_0.111_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230720-sera-500C_0.01_highACE2_counts.csv">Lib2-230720-sera-500C_0.01_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230720-sera-500C_0.043_highACE2_counts.csv">Lib2-230720-sera-500C_0.043_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230720-sera-500C_0.111_highACE2_counts.csv">Lib2-230720-sera-500C_0.111_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230720-sera-503C_0.019_highACE2_counts.csv">Lib2-230720-sera-503C_0.019_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230720-sera-503C_0.073_highACE2_counts.csv">Lib2-230720-sera-503C_0.073_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230720-sera-503C_0.136_highACE2_counts.csv">Lib2-230720-sera-503C_0.136_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230720-no-antibody_control_highACE2_counts.csv">Lib1-230720-no-antibody_control_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230720-no-antibody_control_highACE2_counts.csv">Lib2-230720-no-antibody_control_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230805-sera-493C_0.01_mediumACE2_counts.csv">Lib1-230805-sera-493C_0.01_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230805-sera-493C_0.041_mediumACE2_counts.csv">Lib1-230805-sera-493C_0.041_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230805-sera-493C_0.16_mediumACE2_counts.csv">Lib1-230805-sera-493C_0.16_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230805-sera-498C_0.007_mediumACE2_counts.csv">Lib1-230805-sera-498C_0.007_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230805-sera-498C_0.027_mediumACE2_counts.csv">Lib1-230805-sera-498C_0.027_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230805-sera-498C_0.106_mediumACE2_counts.csv">Lib1-230805-sera-498C_0.106_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230805-sera-500C_0.002_mediumACE2_counts.csv">Lib1-230805-sera-500C_0.002_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230805-sera-500C_0.007_mediumACE2_counts.csv">Lib1-230805-sera-500C_0.007_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230805-sera-500C_0.028_mediumACE2_counts.csv">Lib1-230805-sera-500C_0.028_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230805-sera-501C_0.021_mediumACE2_counts.csv">Lib1-230805-sera-501C_0.021_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230805-sera-501C_0.085_mediumACE2_counts.csv">Lib1-230805-sera-501C_0.085_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230805-sera-501C_0.283_mediumACE2_counts.csv">Lib1-230805-sera-501C_0.283_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230805-sera-503C_0.008_mediumACE2_counts.csv">Lib1-230805-sera-503C_0.008_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230805-sera-503C_0.034_mediumACE2_counts.csv">Lib1-230805-sera-503C_0.034_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230805-sera-503C_0.136_mediumACE2_counts.csv">Lib1-230805-sera-503C_0.136_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230805-no-antibody-control_mediumACE2_counts.csv">Lib1-230805-no-antibody-control_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230805-sera-493C_0.01_mediumACE2_counts.csv">Lib2-230805-sera-493C_0.01_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230805-sera-493C_0.041_mediumACE2_counts.csv">Lib2-230805-sera-493C_0.041_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230805-sera-493C_0.16_mediumACE2_counts.csv">Lib2-230805-sera-493C_0.16_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230805-sera-498C_0.007_mediumACE2_counts.csv">Lib2-230805-sera-498C_0.007_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230805-sera-498C_0.027_mediumACE2_counts.csv">Lib2-230805-sera-498C_0.027_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230805-sera-498C_0.106_mediumACE2_counts.csv">Lib2-230805-sera-498C_0.106_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230805-sera-500C_0.002_mediumACE2_counts.csv">Lib2-230805-sera-500C_0.002_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230805-sera-500C_0.007_mediumACE2_counts.csv">Lib2-230805-sera-500C_0.007_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230805-sera-500C_0.028_mediumACE2_counts.csv">Lib2-230805-sera-500C_0.028_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230805-sera-501C_0.021_mediumACE2_counts.csv">Lib2-230805-sera-501C_0.021_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230805-sera-501C_0.085_mediumACE2_counts.csv">Lib2-230805-sera-501C_0.085_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230805-sera-501C_0.283_mediumACE2_counts.csv">Lib2-230805-sera-501C_0.283_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230805-sera-503C_0.008_mediumACE2_counts.csv">Lib2-230805-sera-503C_0.008_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230805-sera-503C_0.034_mediumACE2_counts.csv">Lib2-230805-sera-503C_0.034_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230805-sera-503C_0.136_mediumACE2_counts.csv">Lib2-230805-sera-503C_0.136_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230805-no-antibody-control_mediumACE2_counts.csv">Lib2-230805-no-antibody-control_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230614-monomeric_ACE2_2.88_counts.csv">Lib1-230614-monomeric_ACE2_2.88</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230614-monomeric_ACE2_8.63_counts.csv">Lib1-230614-monomeric_ACE2_8.63</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230614-monomeric_ACE2_25.9_counts.csv">Lib1-230614-monomeric_ACE2_25.9</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230614-monomeric_ACE2_77.7_counts.csv">Lib1-230614-monomeric_ACE2_77.7</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230614-monomeric_ACE2_233_counts.csv">Lib1-230614-monomeric_ACE2_233</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230614-monomeric_ACE2_2.88_counts.csv">Lib2-230614-monomeric_ACE2_2.88</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230614-monomeric_ACE2_8.63_counts.csv">Lib2-230614-monomeric_ACE2_8.63</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230614-monomeric_ACE2_25.9_counts.csv">Lib2-230614-monomeric_ACE2_25.9</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230614-monomeric_ACE2_77.7_counts.csv">Lib2-230614-monomeric_ACE2_77.7</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230614-monomeric_ACE2_233_counts.csv">Lib2-230614-monomeric_ACE2_233</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-287C_0.013_mediumACE2_counts.csv">Lib1-230815-sera-287C_0.013_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-287C_0.054_mediumACE2_counts.csv">Lib1-230815-sera-287C_0.054_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-287C_0.199_mediumACE2_counts.csv">Lib1-230815-sera-287C_0.199_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-288C_0.013_mediumACE2_counts.csv">Lib1-230815-sera-288C_0.013_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-288C_0.052_mediumACE2_counts.csv">Lib1-230815-sera-288C_0.052_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-288C_0.193_mediumACE2_counts.csv">Lib1-230815-sera-288C_0.193_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-343C_0.009_mediumACE2_counts.csv">Lib1-230815-sera-343C_0.009_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-343C_0.034_mediumACE2_counts.csv">Lib1-230815-sera-343C_0.034_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-343C_0.137_mediumACE2_counts.csv">Lib1-230815-sera-343C_0.137_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-497C_0.016_mediumACE2_counts.csv">Lib1-230815-sera-497C_0.016_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-497C_0.064_mediumACE2_counts.csv">Lib1-230815-sera-497C_0.064_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-497C_0.228_mediumACE2_counts.csv">Lib1-230815-sera-497C_0.228_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-505C_0.018_mediumACE2_counts.csv">Lib1-230815-sera-505C_0.018_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-505C_0.073_mediumACE2_counts.csv">Lib1-230815-sera-505C_0.073_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib1-230815-sera-505C_0.253_mediumACE2_counts.csv">Lib1-230815-sera-505C_0.253_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_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_spike_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-287C_0.013_mediumACE2_counts.csv">Lib2-230815-sera-287C_0.013_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-287C_0.054_mediumACE2_counts.csv">Lib2-230815-sera-287C_0.054_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-287C_0.199_mediumACE2_counts.csv">Lib2-230815-sera-287C_0.199_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-288C_0.013_mediumACE2_counts.csv">Lib2-230815-sera-288C_0.013_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-288C_0.052_mediumACE2_counts.csv">Lib2-230815-sera-288C_0.052_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-288C_0.193_mediumACE2_counts.csv">Lib2-230815-sera-288C_0.193_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-343C_0.009_mediumACE2_counts.csv">Lib2-230815-sera-343C_0.009_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-343C_0.034_mediumACE2_counts.csv">Lib2-230815-sera-343C_0.034_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-343C_0.137_mediumACE2_counts.csv">Lib2-230815-sera-343C_0.137_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-497C_0.016_mediumACE2_counts.csv">Lib2-230815-sera-497C_0.016_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-497C_0.064_mediumACE2_counts.csv">Lib2-230815-sera-497C_0.064_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-497C_0.228_mediumACE2_counts.csv">Lib2-230815-sera-497C_0.228_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-505C_0.018_mediumACE2_counts.csv">Lib2-230815-sera-505C_0.018_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-505C_0.073_mediumACE2_counts.csv">Lib2-230815-sera-505C_0.073_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/barcode_counts/Lib2-230815-sera-505C_0.253_mediumACE2_counts.csv">Lib2-230815-sera-505C_0.253_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_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>
<li><a href="htmls/293T_medium_ACE2_entry_func_effects.html">293T_medium_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>
<li><a href="htmls/293T_medium_ACE2_entry_latent_effects.html">293T_medium_ACE2_entry</a></li>
</ul></details>
</li>
<li><details><summary>Interactive plots of average shifts in functional effects (click triangle to expand/collapse)</summary><ul>
<li><a href="htmls/target_cell_ACE2_expression_comparison_shifts.html">target_cell_ACE2_expression_comparison</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_high_ACE2.html">Lib1-230614_high_ACE2</a></li>
<li><a href="notebooks/func_effects_global_epistasis_Lib2-230614_high_ACE2.html">Lib2-230614_high_ACE2</a></li>
<li><a href="notebooks/func_effects_global_epistasis_Lib1-230614_medium_ACE2.html">Lib1-230614_medium_ACE2</a></li>
<li><a href="notebooks/func_effects_global_epistasis_Lib2-230614_medium_ACE2.html">Lib2-230614_medium_ACE2</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>
<li><a href="notebooks/avg_func_effects_293T_medium_ACE2_entry.html">293T_medium_ACE2_entry</a></li>
</ul></details>
</li>
<li><details><summary>Notebooks fitting shifts in functional effects (click triangle to expand/collapse)</summary><ul>
<li><a href="notebooks/func_effect_shifts_Lib1-230614_ACE2_expression.html">Lib1-230614_ACE2_expression</a></li>
<li><a href="notebooks/func_effect_shifts_Lib2-230614_ACE2_expression.html">Lib2-230614_ACE2_expression</a></li>
</ul></details>
</li>
<li><details><summary>Notebooks averaging shifts in functional effects (click triangle to expand/collapse)</summary><ul>
<li><a href="notebooks/avg_func_effect_shifts_target_cell_ACE2_expression_comparison.html">target_cell_ACE2_expression_comparison</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_spike_DMS/blob/main/results/func_scores/Lib1-230614_high_ACE2_func_scores.csv">Lib1-230614_high_ACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/func_scores/Lib2-230614_high_ACE2_func_scores.csv">Lib2-230614_high_ACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/func_scores/Lib1-230614_medium_ACE2_func_scores.csv">Lib1-230614_medium_ACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/func_scores/Lib2-230614_medium_ACE2_func_scores.csv">Lib2-230614_medium_ACE2</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_spike_DMS/blob/main/results/func_effects/by_selection/Lib1-230614_high_ACE2_func_effects.csv">Lib1-230614_high_ACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/func_effects/by_selection/Lib2-230614_high_ACE2_func_effects.csv">Lib2-230614_high_ACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/func_effects/by_selection/Lib1-230614_medium_ACE2_func_effects.csv">Lib1-230614_medium_ACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/func_effects/by_selection/Lib2-230614_medium_ACE2_func_effects.csv">Lib2-230614_medium_ACE2</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_spike_DMS/blob/main/results/func_effects/averages/293T_high_ACE2_entry_func_effects.csv">293T_high_ACE2_entry</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/func_effects/averages/293T_medium_ACE2_entry_func_effects.csv">293T_medium_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_spike_DMS/blob/main/results/func_effects/averages/293T_high_ACE2_entry_func_effects.csv">293T_high_ACE2_entry</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/func_effects/averages/293T_medium_ACE2_entry_func_effects.csv">293T_medium_ACE2_entry</a></li>
</ul></details>
</li>
<li><details><summary>Per-condition functional effect shifts CSVs (click triangle to expand/collapse)</summary><ul>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/func_effect_shifts/by_comparison/Lib1-230614_ACE2_expression_shifts.csv">Lib1-230614_ACE2_expression</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/func_effect_shifts/by_comparison/Lib2-230614_ACE2_expression_shifts.csv">Lib2-230614_ACE2_expression</a></li>
</ul></details>
</li>
<li><details><summary>Average shifts in 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_spike_DMS/blob/main/results/func_effect_shifts/averages/target_cell_ACE2_expression_comparison_shifts.csv">target_cell_ACE2_expression_comparison</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_highACE2_mut_effect.html">sera_493C_highACE2</a></li>
<li><a href="htmls/sera_498C_highACE2_mut_effect.html">sera_498C_highACE2</a></li>
<li><a href="htmls/sera_500C_highACE2_mut_effect.html">sera_500C_highACE2</a></li>
<li><a href="htmls/sera_503C_highACE2_mut_effect.html">sera_503C_highACE2</a></li>
<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_501C_mediumACE2_mut_effect.html">sera_501C_mediumACE2</a></li>
<li><a href="htmls/sera_503C_mediumACE2_mut_effect.html">sera_503C_mediumACE2</a></li>
<li><a href="htmls/sera_287C_mediumACE2_mut_effect.html">sera_287C_mediumACE2</a></li>
<li><a href="htmls/sera_288C_mediumACE2_mut_effect.html">sera_288C_mediumACE2</a></li>
<li><a href="htmls/sera_343C_mediumACE2_mut_effect.html">sera_343C_mediumACE2</a></li>
<li><a href="htmls/sera_497C_mediumACE2_mut_effect.html">sera_497C_mediumACE2</a></li>
<li><a href="htmls/sera_505C_mediumACE2_mut_effect.html">sera_505C_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_Lib1-230720-sera-493C_highACE2.html">Lib1-230720-sera-493C_highACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib2-230720-sera-493C_highACE2.html">Lib2-230720-sera-493C_highACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib1-230720-sera-498C_highACE2.html">Lib1-230720-sera-498C_highACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib2-230720-sera-498C_highACE2.html">Lib2-230720-sera-498C_highACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib1-230720-sera-500C_highACE2.html">Lib1-230720-sera-500C_highACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib2-230720-sera-500C_highACE2.html">Lib2-230720-sera-500C_highACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib1-230729-sera-503C_highACE2.html">Lib1-230729-sera-503C_highACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib2-230720-sera-503C_highACE2.html">Lib2-230720-sera-503C_highACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib1-230805-sera-493C_mediumACE2.html">Lib1-230805-sera-493C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib2-230805-sera-493C_mediumACE2.html">Lib2-230805-sera-493C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib1-230805-sera-498C_mediumACE2.html">Lib1-230805-sera-498C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib2-230805-sera-498C_mediumACE2.html">Lib2-230805-sera-498C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib1-230805-sera-500C_mediumACE2.html">Lib1-230805-sera-500C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib2-230805-sera-500C_mediumACE2.html">Lib2-230805-sera-500C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib1-230805-sera-501C_mediumACE2.html">Lib1-230805-sera-501C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib2-230805-sera-501C_mediumACE2.html">Lib2-230805-sera-501C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib1-230805-sera-503C_mediumACE2.html">Lib1-230805-sera-503C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib2-230805-sera-503C_mediumACE2.html">Lib2-230805-sera-503C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib1-230815-sera-287C_mediumACE2.html">Lib1-230815-sera-287C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib2-230815-sera-287C_mediumACE2.html">Lib2-230815-sera-287C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib1-230815-sera-288C_mediumACE2.html">Lib1-230815-sera-288C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib2-230815-sera-288C_mediumACE2.html">Lib2-230815-sera-288C_mediumACE2</a></li>
<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-497C_mediumACE2.html">Lib1-230815-sera-497C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib2-230815-sera-497C_mediumACE2.html">Lib2-230815-sera-497C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib1-230815-sera-505C_mediumACE2.html">Lib1-230815-sera-505C_mediumACE2</a></li>
<li><a href="notebooks/fit_escape_antibody_escape_Lib2-230815-sera-505C_mediumACE2.html">Lib2-230815-sera-505C_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_highACE2.html">sera_493C_highACE2</a></li>
<li><a href="notebooks/avg_escape_antibody_escape_sera_498C_highACE2.html">sera_498C_highACE2</a></li>
<li><a href="notebooks/avg_escape_antibody_escape_sera_500C_highACE2.html">sera_500C_highACE2</a></li>
<li><a href="notebooks/avg_escape_antibody_escape_sera_503C_highACE2.html">sera_503C_highACE2</a></li>
<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_501C_mediumACE2.html">sera_501C_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_287C_mediumACE2.html">sera_287C_mediumACE2</a></li>
<li><a href="notebooks/avg_escape_antibody_escape_sera_288C_mediumACE2.html">sera_288C_mediumACE2</a></li>
<li><a href="notebooks/avg_escape_antibody_escape_sera_343C_mediumACE2.html">sera_343C_mediumACE2</a></li>
<li><a href="notebooks/avg_escape_antibody_escape_sera_497C_mediumACE2.html">sera_497C_mediumACE2</a></li>
<li><a href="notebooks/avg_escape_antibody_escape_sera_505C_mediumACE2.html">sera_505C_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_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230720-sera-493C_highACE2/Lib1-230720-sera-493C_0.045_highACE2_prob_escape.csv">Lib1-230720-sera-493C_highACE2 Lib1-230720-sera-493C_0.045_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230720-sera-493C_highACE2/Lib1-230720-sera-493C_0.091_highACE2_prob_escape.csv">Lib1-230720-sera-493C_highACE2 Lib1-230720-sera-493C_0.091_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230720-sera-493C_highACE2/Lib1-230720-sera-493C_0.16_highACE2_prob_escape.csv">Lib1-230720-sera-493C_highACE2 Lib1-230720-sera-493C_0.16_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230720-sera-493C_highACE2/Lib2-230720-sera-493C_0.045_highACE2_prob_escape.csv">Lib2-230720-sera-493C_highACE2 Lib2-230720-sera-493C_0.045_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230720-sera-493C_highACE2/Lib2-230720-sera-493C_0.091_highACE2_prob_escape.csv">Lib2-230720-sera-493C_highACE2 Lib2-230720-sera-493C_0.091_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230720-sera-493C_highACE2/Lib2-230720-sera-493C_0.16_highACE2_prob_escape.csv">Lib2-230720-sera-493C_highACE2 Lib2-230720-sera-493C_0.16_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230720-sera-498C_highACE2/Lib1-230720-sera-498C_0.015_highACE2_prob_escape.csv">Lib1-230720-sera-498C_highACE2 Lib1-230720-sera-498C_0.015_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230720-sera-498C_highACE2/Lib1-230720-sera-498C_0.058_highACE2_prob_escape.csv">Lib1-230720-sera-498C_highACE2 Lib1-230720-sera-498C_0.058_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230720-sera-498C_highACE2/Lib1-230720-sera-498C_0.197_highACE2_prob_escape.csv">Lib1-230720-sera-498C_highACE2 Lib1-230720-sera-498C_0.197_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230720-sera-498C_highACE2/Lib2-230720-sera-498C_0.015_highACE2_prob_escape.csv">Lib2-230720-sera-498C_highACE2 Lib2-230720-sera-498C_0.015_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230720-sera-498C_highACE2/Lib2-230720-sera-498C_0.058_highACE2_prob_escape.csv">Lib2-230720-sera-498C_highACE2 Lib2-230720-sera-498C_0.058_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230720-sera-498C_highACE2/Lib2-230720-sera-498C_0.197_highACE2_prob_escape.csv">Lib2-230720-sera-498C_highACE2 Lib2-230720-sera-498C_0.197_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230720-sera-500C_highACE2/Lib1-230720-sera-500C_0.01_highACE2_prob_escape.csv">Lib1-230720-sera-500C_highACE2 Lib1-230720-sera-500C_0.01_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230720-sera-500C_highACE2/Lib1-230720-sera-500C_0.043_highACE2_prob_escape.csv">Lib1-230720-sera-500C_highACE2 Lib1-230720-sera-500C_0.043_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230720-sera-500C_highACE2/Lib1-230720-sera-500C_0.111_highACE2_prob_escape.csv">Lib1-230720-sera-500C_highACE2 Lib1-230720-sera-500C_0.111_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230720-sera-500C_highACE2/Lib2-230720-sera-500C_0.01_highACE2_prob_escape.csv">Lib2-230720-sera-500C_highACE2 Lib2-230720-sera-500C_0.01_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230720-sera-500C_highACE2/Lib2-230720-sera-500C_0.043_highACE2_prob_escape.csv">Lib2-230720-sera-500C_highACE2 Lib2-230720-sera-500C_0.043_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230720-sera-500C_highACE2/Lib2-230720-sera-500C_0.111_highACE2_prob_escape.csv">Lib2-230720-sera-500C_highACE2 Lib2-230720-sera-500C_0.111_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230729-sera-503C_highACE2/Lib1-230729-sera-503C_0.008483_highACE2_prob_escape.csv">Lib1-230729-sera-503C_highACE2 Lib1-230729-sera-503C_0.008483_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230729-sera-503C_highACE2/Lib1-230729-sera-503C_0.033932_highACE2_prob_escape.csv">Lib1-230729-sera-503C_highACE2 Lib1-230729-sera-503C_0.033932_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230729-sera-503C_highACE2/Lib1-230729-sera-503C_0.135728_highACE2_prob_escape.csv">Lib1-230729-sera-503C_highACE2 Lib1-230729-sera-503C_0.135728_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230720-sera-503C_highACE2/Lib2-230720-sera-503C_0.019_highACE2_prob_escape.csv">Lib2-230720-sera-503C_highACE2 Lib2-230720-sera-503C_0.019_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230720-sera-503C_highACE2/Lib2-230720-sera-503C_0.073_highACE2_prob_escape.csv">Lib2-230720-sera-503C_highACE2 Lib2-230720-sera-503C_0.073_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230720-sera-503C_highACE2/Lib2-230720-sera-503C_0.136_highACE2_prob_escape.csv">Lib2-230720-sera-503C_highACE2 Lib2-230720-sera-503C_0.136_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230805-sera-493C_mediumACE2/Lib1-230805-sera-493C_0.01_mediumACE2_prob_escape.csv">Lib1-230805-sera-493C_mediumACE2 Lib1-230805-sera-493C_0.01_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230805-sera-493C_mediumACE2/Lib1-230805-sera-493C_0.041_mediumACE2_prob_escape.csv">Lib1-230805-sera-493C_mediumACE2 Lib1-230805-sera-493C_0.041_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230805-sera-493C_mediumACE2/Lib1-230805-sera-493C_0.16_mediumACE2_prob_escape.csv">Lib1-230805-sera-493C_mediumACE2 Lib1-230805-sera-493C_0.16_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230805-sera-493C_mediumACE2/Lib2-230805-sera-493C_0.01_mediumACE2_prob_escape.csv">Lib2-230805-sera-493C_mediumACE2 Lib2-230805-sera-493C_0.01_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230805-sera-493C_mediumACE2/Lib2-230805-sera-493C_0.041_mediumACE2_prob_escape.csv">Lib2-230805-sera-493C_mediumACE2 Lib2-230805-sera-493C_0.041_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230805-sera-493C_mediumACE2/Lib2-230805-sera-493C_0.16_mediumACE2_prob_escape.csv">Lib2-230805-sera-493C_mediumACE2 Lib2-230805-sera-493C_0.16_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230805-sera-498C_mediumACE2/Lib1-230805-sera-498C_0.007_mediumACE2_prob_escape.csv">Lib1-230805-sera-498C_mediumACE2 Lib1-230805-sera-498C_0.007_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230805-sera-498C_mediumACE2/Lib1-230805-sera-498C_0.027_mediumACE2_prob_escape.csv">Lib1-230805-sera-498C_mediumACE2 Lib1-230805-sera-498C_0.027_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230805-sera-498C_mediumACE2/Lib1-230805-sera-498C_0.106_mediumACE2_prob_escape.csv">Lib1-230805-sera-498C_mediumACE2 Lib1-230805-sera-498C_0.106_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230805-sera-498C_mediumACE2/Lib2-230805-sera-498C_0.007_mediumACE2_prob_escape.csv">Lib2-230805-sera-498C_mediumACE2 Lib2-230805-sera-498C_0.007_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230805-sera-498C_mediumACE2/Lib2-230805-sera-498C_0.027_mediumACE2_prob_escape.csv">Lib2-230805-sera-498C_mediumACE2 Lib2-230805-sera-498C_0.027_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230805-sera-498C_mediumACE2/Lib2-230805-sera-498C_0.106_mediumACE2_prob_escape.csv">Lib2-230805-sera-498C_mediumACE2 Lib2-230805-sera-498C_0.106_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230805-sera-500C_mediumACE2/Lib1-230805-sera-500C_0.002_mediumACE2_prob_escape.csv">Lib1-230805-sera-500C_mediumACE2 Lib1-230805-sera-500C_0.002_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230805-sera-500C_mediumACE2/Lib1-230805-sera-500C_0.007_mediumACE2_prob_escape.csv">Lib1-230805-sera-500C_mediumACE2 Lib1-230805-sera-500C_0.007_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230805-sera-500C_mediumACE2/Lib1-230805-sera-500C_0.028_mediumACE2_prob_escape.csv">Lib1-230805-sera-500C_mediumACE2 Lib1-230805-sera-500C_0.028_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230805-sera-500C_mediumACE2/Lib2-230805-sera-500C_0.002_mediumACE2_prob_escape.csv">Lib2-230805-sera-500C_mediumACE2 Lib2-230805-sera-500C_0.002_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230805-sera-500C_mediumACE2/Lib2-230805-sera-500C_0.007_mediumACE2_prob_escape.csv">Lib2-230805-sera-500C_mediumACE2 Lib2-230805-sera-500C_0.007_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230805-sera-500C_mediumACE2/Lib2-230805-sera-500C_0.028_mediumACE2_prob_escape.csv">Lib2-230805-sera-500C_mediumACE2 Lib2-230805-sera-500C_0.028_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230805-sera-501C_mediumACE2/Lib1-230805-sera-501C_0.021_mediumACE2_prob_escape.csv">Lib1-230805-sera-501C_mediumACE2 Lib1-230805-sera-501C_0.021_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230805-sera-501C_mediumACE2/Lib1-230805-sera-501C_0.085_mediumACE2_prob_escape.csv">Lib1-230805-sera-501C_mediumACE2 Lib1-230805-sera-501C_0.085_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230805-sera-501C_mediumACE2/Lib1-230805-sera-501C_0.283_mediumACE2_prob_escape.csv">Lib1-230805-sera-501C_mediumACE2 Lib1-230805-sera-501C_0.283_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230805-sera-501C_mediumACE2/Lib2-230805-sera-501C_0.021_mediumACE2_prob_escape.csv">Lib2-230805-sera-501C_mediumACE2 Lib2-230805-sera-501C_0.021_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230805-sera-501C_mediumACE2/Lib2-230805-sera-501C_0.085_mediumACE2_prob_escape.csv">Lib2-230805-sera-501C_mediumACE2 Lib2-230805-sera-501C_0.085_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230805-sera-501C_mediumACE2/Lib2-230805-sera-501C_0.283_mediumACE2_prob_escape.csv">Lib2-230805-sera-501C_mediumACE2 Lib2-230805-sera-501C_0.283_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230805-sera-503C_mediumACE2/Lib1-230805-sera-503C_0.008_mediumACE2_prob_escape.csv">Lib1-230805-sera-503C_mediumACE2 Lib1-230805-sera-503C_0.008_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230805-sera-503C_mediumACE2/Lib1-230805-sera-503C_0.034_mediumACE2_prob_escape.csv">Lib1-230805-sera-503C_mediumACE2 Lib1-230805-sera-503C_0.034_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230805-sera-503C_mediumACE2/Lib1-230805-sera-503C_0.136_mediumACE2_prob_escape.csv">Lib1-230805-sera-503C_mediumACE2 Lib1-230805-sera-503C_0.136_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230805-sera-503C_mediumACE2/Lib2-230805-sera-503C_0.008_mediumACE2_prob_escape.csv">Lib2-230805-sera-503C_mediumACE2 Lib2-230805-sera-503C_0.008_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230805-sera-503C_mediumACE2/Lib2-230805-sera-503C_0.034_mediumACE2_prob_escape.csv">Lib2-230805-sera-503C_mediumACE2 Lib2-230805-sera-503C_0.034_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230805-sera-503C_mediumACE2/Lib2-230805-sera-503C_0.136_mediumACE2_prob_escape.csv">Lib2-230805-sera-503C_mediumACE2 Lib2-230805-sera-503C_0.136_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-287C_mediumACE2/Lib1-230815-sera-287C_0.013_mediumACE2_prob_escape.csv">Lib1-230815-sera-287C_mediumACE2 Lib1-230815-sera-287C_0.013_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-287C_mediumACE2/Lib1-230815-sera-287C_0.054_mediumACE2_prob_escape.csv">Lib1-230815-sera-287C_mediumACE2 Lib1-230815-sera-287C_0.054_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-287C_mediumACE2/Lib1-230815-sera-287C_0.199_mediumACE2_prob_escape.csv">Lib1-230815-sera-287C_mediumACE2 Lib1-230815-sera-287C_0.199_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-287C_mediumACE2/Lib2-230815-sera-287C_0.013_mediumACE2_prob_escape.csv">Lib2-230815-sera-287C_mediumACE2 Lib2-230815-sera-287C_0.013_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-287C_mediumACE2/Lib2-230815-sera-287C_0.054_mediumACE2_prob_escape.csv">Lib2-230815-sera-287C_mediumACE2 Lib2-230815-sera-287C_0.054_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-287C_mediumACE2/Lib2-230815-sera-287C_0.199_mediumACE2_prob_escape.csv">Lib2-230815-sera-287C_mediumACE2 Lib2-230815-sera-287C_0.199_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-288C_mediumACE2/Lib1-230815-sera-288C_0.013_mediumACE2_prob_escape.csv">Lib1-230815-sera-288C_mediumACE2 Lib1-230815-sera-288C_0.013_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-288C_mediumACE2/Lib1-230815-sera-288C_0.052_mediumACE2_prob_escape.csv">Lib1-230815-sera-288C_mediumACE2 Lib1-230815-sera-288C_0.052_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-288C_mediumACE2/Lib1-230815-sera-288C_0.193_mediumACE2_prob_escape.csv">Lib1-230815-sera-288C_mediumACE2 Lib1-230815-sera-288C_0.193_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-288C_mediumACE2/Lib2-230815-sera-288C_0.013_mediumACE2_prob_escape.csv">Lib2-230815-sera-288C_mediumACE2 Lib2-230815-sera-288C_0.013_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-288C_mediumACE2/Lib2-230815-sera-288C_0.052_mediumACE2_prob_escape.csv">Lib2-230815-sera-288C_mediumACE2 Lib2-230815-sera-288C_0.052_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-288C_mediumACE2/Lib2-230815-sera-288C_0.193_mediumACE2_prob_escape.csv">Lib2-230815-sera-288C_mediumACE2 Lib2-230815-sera-288C_0.193_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-343C_mediumACE2/Lib1-230815-sera-343C_0.009_mediumACE2_prob_escape.csv">Lib1-230815-sera-343C_mediumACE2 Lib1-230815-sera-343C_0.009_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-343C_mediumACE2/Lib1-230815-sera-343C_0.034_mediumACE2_prob_escape.csv">Lib1-230815-sera-343C_mediumACE2 Lib1-230815-sera-343C_0.034_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-343C_mediumACE2/Lib1-230815-sera-343C_0.137_mediumACE2_prob_escape.csv">Lib1-230815-sera-343C_mediumACE2 Lib1-230815-sera-343C_0.137_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-343C_mediumACE2/Lib2-230815-sera-343C_0.009_mediumACE2_prob_escape.csv">Lib2-230815-sera-343C_mediumACE2 Lib2-230815-sera-343C_0.009_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-343C_mediumACE2/Lib2-230815-sera-343C_0.034_mediumACE2_prob_escape.csv">Lib2-230815-sera-343C_mediumACE2 Lib2-230815-sera-343C_0.034_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-343C_mediumACE2/Lib2-230815-sera-343C_0.137_mediumACE2_prob_escape.csv">Lib2-230815-sera-343C_mediumACE2 Lib2-230815-sera-343C_0.137_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-497C_mediumACE2/Lib1-230815-sera-497C_0.016_mediumACE2_prob_escape.csv">Lib1-230815-sera-497C_mediumACE2 Lib1-230815-sera-497C_0.016_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-497C_mediumACE2/Lib1-230815-sera-497C_0.064_mediumACE2_prob_escape.csv">Lib1-230815-sera-497C_mediumACE2 Lib1-230815-sera-497C_0.064_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-497C_mediumACE2/Lib1-230815-sera-497C_0.228_mediumACE2_prob_escape.csv">Lib1-230815-sera-497C_mediumACE2 Lib1-230815-sera-497C_0.228_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-497C_mediumACE2/Lib2-230815-sera-497C_0.016_mediumACE2_prob_escape.csv">Lib2-230815-sera-497C_mediumACE2 Lib2-230815-sera-497C_0.016_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-497C_mediumACE2/Lib2-230815-sera-497C_0.064_mediumACE2_prob_escape.csv">Lib2-230815-sera-497C_mediumACE2 Lib2-230815-sera-497C_0.064_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-497C_mediumACE2/Lib2-230815-sera-497C_0.228_mediumACE2_prob_escape.csv">Lib2-230815-sera-497C_mediumACE2 Lib2-230815-sera-497C_0.228_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-505C_mediumACE2/Lib1-230815-sera-505C_0.018_mediumACE2_prob_escape.csv">Lib1-230815-sera-505C_mediumACE2 Lib1-230815-sera-505C_0.018_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-505C_mediumACE2/Lib1-230815-sera-505C_0.073_mediumACE2_prob_escape.csv">Lib1-230815-sera-505C_mediumACE2 Lib1-230815-sera-505C_0.073_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib1-230815-sera-505C_mediumACE2/Lib1-230815-sera-505C_0.253_mediumACE2_prob_escape.csv">Lib1-230815-sera-505C_mediumACE2 Lib1-230815-sera-505C_0.253_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-505C_mediumACE2/Lib2-230815-sera-505C_0.018_mediumACE2_prob_escape.csv">Lib2-230815-sera-505C_mediumACE2 Lib2-230815-sera-505C_0.018_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-505C_mediumACE2/Lib2-230815-sera-505C_0.073_mediumACE2_prob_escape.csv">Lib2-230815-sera-505C_mediumACE2 Lib2-230815-sera-505C_0.073_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/by_selection/Lib2-230815-sera-505C_mediumACE2/Lib2-230815-sera-505C_0.253_mediumACE2_prob_escape.csv">Lib2-230815-sera-505C_mediumACE2 Lib2-230815-sera-505C_0.253_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_spike_DMS/blob/main/results/antibody_escape/averages/sera_493C_highACE2_mut_effect.csv">sera_493C_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/averages/sera_498C_highACE2_mut_effect.csv">sera_498C_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/averages/sera_500C_highACE2_mut_effect.csv">sera_500C_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/averages/sera_503C_highACE2_mut_effect.csv">sera_503C_highACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_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_spike_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_spike_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_spike_DMS/blob/main/results/antibody_escape/averages/sera_501C_mediumACE2_mut_effect.csv">sera_501C_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_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_spike_DMS/blob/main/results/antibody_escape/averages/sera_287C_mediumACE2_mut_effect.csv">sera_287C_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/averages/sera_288C_mediumACE2_mut_effect.csv">sera_288C_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/averages/sera_343C_mediumACE2_mut_effect.csv">sera_343C_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/averages/sera_497C_mediumACE2_mut_effect.csv">sera_497C_mediumACE2</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/antibody_escape/averages/sera_505C_mediumACE2_mut_effect.csv">sera_505C_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>
</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_Lib1-230614-monomeric_ACE2.html">Lib1-230614-monomeric_ACE2</a></li>
<li><a href="notebooks/fit_escape_ACE2_binding_Lib2-230614-monomeric_ACE2.html">Lib2-230614-monomeric_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>
</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_spike_DMS/blob/main/results/ACE2_binding/by_selection/Lib1-230614-monomeric_ACE2/Lib1-230614-monomeric_ACE2_2.88_prob_escape.csv">Lib1-230614-monomeric_ACE2 Lib1-230614-monomeric_ACE2_2.88</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/ACE2_binding/by_selection/Lib1-230614-monomeric_ACE2/Lib1-230614-monomeric_ACE2_8.63_prob_escape.csv">Lib1-230614-monomeric_ACE2 Lib1-230614-monomeric_ACE2_8.63</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/ACE2_binding/by_selection/Lib1-230614-monomeric_ACE2/Lib1-230614-monomeric_ACE2_25.9_prob_escape.csv">Lib1-230614-monomeric_ACE2 Lib1-230614-monomeric_ACE2_25.9</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/ACE2_binding/by_selection/Lib1-230614-monomeric_ACE2/Lib1-230614-monomeric_ACE2_77.7_prob_escape.csv">Lib1-230614-monomeric_ACE2 Lib1-230614-monomeric_ACE2_77.7</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/ACE2_binding/by_selection/Lib1-230614-monomeric_ACE2/Lib1-230614-monomeric_ACE2_233_prob_escape.csv">Lib1-230614-monomeric_ACE2 Lib1-230614-monomeric_ACE2_233</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/ACE2_binding/by_selection/Lib2-230614-monomeric_ACE2/Lib2-230614-monomeric_ACE2_2.88_prob_escape.csv">Lib2-230614-monomeric_ACE2 Lib2-230614-monomeric_ACE2_2.88</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/ACE2_binding/by_selection/Lib2-230614-monomeric_ACE2/Lib2-230614-monomeric_ACE2_8.63_prob_escape.csv">Lib2-230614-monomeric_ACE2 Lib2-230614-monomeric_ACE2_8.63</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/ACE2_binding/by_selection/Lib2-230614-monomeric_ACE2/Lib2-230614-monomeric_ACE2_25.9_prob_escape.csv">Lib2-230614-monomeric_ACE2 Lib2-230614-monomeric_ACE2_25.9</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/ACE2_binding/by_selection/Lib2-230614-monomeric_ACE2/Lib2-230614-monomeric_ACE2_77.7_prob_escape.csv">Lib2-230614-monomeric_ACE2 Lib2-230614-monomeric_ACE2_77.7</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/ACE2_binding/by_selection/Lib2-230614-monomeric_ACE2/Lib2-230614-monomeric_ACE2_233_prob_escape.csv">Lib2-230614-monomeric_ACE2 Lib2-230614-monomeric_ACE2_233</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_spike_DMS/blob/main/results/ACE2_binding/averages/monomeric_ACE2_mut_effect.csv">monomeric_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_spike_DMS/blob/main/results/summaries/summary.csv">CSV summarizing overall results</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/summaries/per_antibody_escape.csv">CSV summarizing per-antibody results</a></li>
</ul>
<h2 id="additional-files-and-charts">Additional files and charts</h2>
<h4 id="analysis-of-escape-and-other-properties-at-key-sites">Analysis of escape and other properties at key sites</h4>
<ul>
<li><a href="notebooks/escape_at_key_sites.html">Notebook making logo plots of escape at key sites</a></li>
<li><a href="notebooks/binding_vs_escape.html">Notebook comparing binding vs escape at key sites</a></li>
</ul>
<h4 id="analysis-of-ace2-binding-data-and-comparison-to-other-experiments">Analysis of ACE2 binding data and comparison to other experiments</h4>
<ul>
<li><details><summary>Interactive charts (click triangle to expand/collapse)</summary><ul>
<li><a href="htmls/binding_corr.html">Correlations among experiments</a></li>
<li><a href="htmls/binding_dist.html">Distribution of RBD and non-RBD ACE2 binding</a></li>
<li><a href="htmls/binding_entry_corr.html">Correlation of ACE2 binding to viral entry</a></li>
<li><a href="htmls/binding_ecape_corr.html">Correlation of ACE2 binding to viral escape</a></li>
</ul></details>
</li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/binding_comparison/merged_binding.csv">CSV of ACE2 binding from different experiments</a></li>
</ul>
<h4 id="comparison-of-escape-in-medium-and-high-ace2-cells">Comparison of escape in medium and high ACE2 cells</h4>
<ul>
<li><a href="htmls/compare_high_medium_ace2_escape.html">Interactive chart comparing escape</a></li>
</ul>
<h4 id="comparison-of-escape-in-full-spike-and-rbd-deep-mutational-scans">Comparison of escape in full-spike and RBD deep mutational scans</h4>
<ul>
<li><a href="htmls/compare_spike_rbd_escape.html">Interactive chart comparing escape in spike vs RBD scans</a></li>
<li><a href="htmls/rbd_vs_non_rbd_escape.html">Distributions of escape by RBD and non-RBD mutations in spike scan</a></li>
</ul>
<h4 id="dms-measurements-versus-clade-growth-xbb-clades">DMS measurements versus clade growth (XBB clades)</h4>
<ul>
<li><details><summary>Comparison for current_dms (XBB clades) (click triangle to expand/collapse)</summary><ul>
<li><a href="htmls/current_dms_clade_pair_growth.html">Correlation of change in clade growth versus phenotype for clade pairs</a></li>
<li><a href="htmls/current_dms_ols_clade_pair_growth.html">OLS change in clade growth versus phenotype for clade pairs</a></li>
<li><a href="htmls/current_dms_clade_growth.html">Correlation of absolute clade growth versus phenotype</a></li>
<li><a href="notebooks/current_dms_compare_natural.html">Notebook comparing change in clade growth to change in phenotype</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/compare_natural/current_dms_clade_pair_growth.csv">CSV with data for comparison of changes in growth vs phenotype for clade pairs</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/compare_natural/current_dms_clade_growth.csv">CSV with phenotypes and growth for all individual clades</a></li>
</ul></details>
</li>
<li><details><summary>Comparison for yeast_RBD_DMS (XBB clades) (click triangle to expand/collapse)</summary><ul>
<li><a href="htmls/yeast_RBD_DMS_clade_pair_growth.html">Correlation of change in clade growth versus phenotype for clade pairs</a></li>
<li><a href="htmls/yeast_RBD_DMS_ols_clade_pair_growth.html">OLS change in clade growth versus phenotype for clade pairs</a></li>
<li><a href="htmls/yeast_RBD_DMS_clade_growth.html">Correlation of absolute clade growth versus phenotype</a></li>
<li><a href="notebooks/yeast_RBD_DMS_compare_natural.html">Notebook comparing change in clade growth to change in phenotype</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/compare_natural/yeast_RBD_DMS_clade_pair_growth.csv">CSV with data for comparison of changes in growth vs phenotype for clade pairs</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/compare_natural/yeast_RBD_DMS_clade_growth.csv">CSV with phenotypes and growth for all individual clades</a></li>
</ul></details>
</li>
<li><details><summary>Comparison for muts_from_Wuhan-Hu-1 (XBB clades) (click triangle to expand/collapse)</summary><ul>
<li><a href="htmls/muts_from_Wuhan-Hu-1_clade_pair_growth.html">Correlation of change in clade growth versus phenotype for clade pairs</a></li>
<li><a href="htmls/muts_from_Wuhan-Hu-1_ols_clade_pair_growth.html">OLS change in clade growth versus phenotype for clade pairs</a></li>
<li><a href="htmls/muts_from_Wuhan-Hu-1_clade_growth.html">Correlation of absolute clade growth versus phenotype</a></li>
<li><a href="notebooks/muts_from_Wuhan-Hu-1_compare_natural.html">Notebook comparing change in clade growth to change in phenotype</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/compare_natural/muts_from_Wuhan-Hu-1_clade_pair_growth.csv">CSV with data for comparison of changes in growth vs phenotype for clade pairs</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/compare_natural/muts_from_Wuhan-Hu-1_clade_growth.csv">CSV with phenotypes and growth for all individual clades</a></li>
</ul></details>
</li>
<li><details><summary>Comparison for EVEscape (XBB clades) (click triangle to expand/collapse)</summary><ul>
<li><a href="htmls/EVEscape_clade_pair_growth.html">Correlation of change in clade growth versus phenotype for clade pairs</a></li>
<li><a href="htmls/EVEscape_ols_clade_pair_growth.html">OLS change in clade growth versus phenotype for clade pairs</a></li>
<li><a href="htmls/EVEscape_clade_growth.html">Correlation of absolute clade growth versus phenotype</a></li>
<li><a href="notebooks/EVEscape_compare_natural.html">Notebook comparing change in clade growth to change in phenotype</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/compare_natural/EVEscape_clade_pair_growth.csv">CSV with data for comparison of changes in growth vs phenotype for clade pairs</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/compare_natural/EVEscape_clade_growth.csv">CSV with phenotypes and growth for all individual clades</a></li>
</ul></details>
</li>
<li><details><summary>Comparison for EVEscape_components (XBB clades) (click triangle to expand/collapse)</summary><ul>
<li><a href="htmls/EVEscape_components_clade_pair_growth.html">Correlation of change in clade growth versus phenotype for clade pairs</a></li>
<li><a href="htmls/EVEscape_components_ols_clade_pair_growth.html">OLS change in clade growth versus phenotype for clade pairs</a></li>
<li><a href="htmls/EVEscape_components_clade_growth.html">Correlation of absolute clade growth versus phenotype</a></li>
<li><a href="notebooks/EVEscape_components_compare_natural.html">Notebook comparing change in clade growth to change in phenotype</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/compare_natural/EVEscape_components_clade_pair_growth.csv">CSV with data for comparison of changes in growth vs phenotype for clade pairs</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/compare_natural/EVEscape_components_clade_growth.csv">CSV with phenotypes and growth for all individual clades</a></li>
</ul></details>
</li>
</ul>
<h4 id="dms-measurements-versus-clade-growth-ba2-ba5-and-xbb-clades">DMS measurements versus clade growth (BA.2, BA.5, and XBB clades)</h4>
<ul>
<li><details><summary>Comparison for current_dms (BA.2, BA.5, and XBB clades) (click triangle to expand/collapse)</summary><ul>
<li><a href="htmls/current_dms_clade_pair_growth_ba2_ba5_xbb.html">Correlation of change in clade growth versus phenotype for clade pairs</a></li>
<li><a href="htmls/current_dms_ols_clade_pair_growth_ba2_ba5_xbb.html">OLS change in clade growth versus phenotype for clade pairs</a></li>
<li><a href="htmls/current_dms_clade_growth_ba2_ba5_xbb.html">Correlation of absolute clade growth versus phenotype</a></li>
<li><a href="notebooks/current_dms_compare_natural_ba2_ba5_xbb.html">Notebook comparing change in clade growth to change in phenotype</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/compare_natural/current_dms_clade_pair_growth_ba2_ba5_xbb.csv">CSV with data for comparison of changes in growth vs phenotype for clade pairs</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/compare_natural/current_dms_clade_growth_ba2_ba5_xbb.csv">CSV with phenotypes and growth for all individual clades</a></li>
</ul></details>
</li>
<li><details><summary>Comparison for yeast_RBD_DMS (BA.2, BA.5, and XBB clades) (click triangle to expand/collapse)</summary><ul>
<li><a href="htmls/yeast_RBD_DMS_clade_pair_growth_ba2_ba5_xbb.html">Correlation of change in clade growth versus phenotype for clade pairs</a></li>
<li><a href="htmls/yeast_RBD_DMS_ols_clade_pair_growth_ba2_ba5_xbb.html">OLS change in clade growth versus phenotype for clade pairs</a></li>
<li><a href="htmls/yeast_RBD_DMS_clade_growth_ba2_ba5_xbb.html">Correlation of absolute clade growth versus phenotype</a></li>
<li><a href="notebooks/yeast_RBD_DMS_compare_natural_ba2_ba5_xbb.html">Notebook comparing change in clade growth to change in phenotype</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/compare_natural/yeast_RBD_DMS_clade_pair_growth_ba2_ba5_xbb.csv">CSV with data for comparison of changes in growth vs phenotype for clade pairs</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/compare_natural/yeast_RBD_DMS_clade_growth_ba2_ba5_xbb.csv">CSV with phenotypes and growth for all individual clades</a></li>
</ul></details>
</li>
<li><details><summary>Comparison for muts_from_Wuhan-Hu-1 (BA.2, BA.5, and XBB clades) (click triangle to expand/collapse)</summary><ul>
<li><a href="htmls/muts_from_Wuhan-Hu-1_clade_pair_growth_ba2_ba5_xbb.html">Correlation of change in clade growth versus phenotype for clade pairs</a></li>
<li><a href="htmls/muts_from_Wuhan-Hu-1_ols_clade_pair_growth_ba2_ba5_xbb.html">OLS change in clade growth versus phenotype for clade pairs</a></li>
<li><a href="htmls/muts_from_Wuhan-Hu-1_clade_growth_ba2_ba5_xbb.html">Correlation of absolute clade growth versus phenotype</a></li>
<li><a href="notebooks/muts_from_Wuhan-Hu-1_compare_natural_ba2_ba5_xbb.html">Notebook comparing change in clade growth to change in phenotype</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/compare_natural/muts_from_Wuhan-Hu-1_clade_pair_growth_ba2_ba5_xbb.csv">CSV with data for comparison of changes in growth vs phenotype for clade pairs</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/compare_natural/muts_from_Wuhan-Hu-1_clade_growth_ba2_ba5_xbb.csv">CSV with phenotypes and growth for all individual clades</a></li>
</ul></details>
</li>
<li><details><summary>Comparison for EVEscape (BA.2, BA.5, and XBB clades) (click triangle to expand/collapse)</summary><ul>
<li><a href="htmls/EVEscape_clade_pair_growth_ba2_ba5_xbb.html">Correlation of change in clade growth versus phenotype for clade pairs</a></li>
<li><a href="htmls/EVEscape_ols_clade_pair_growth_ba2_ba5_xbb.html">OLS change in clade growth versus phenotype for clade pairs</a></li>
<li><a href="htmls/EVEscape_clade_growth_ba2_ba5_xbb.html">Correlation of absolute clade growth versus phenotype</a></li>
<li><a href="notebooks/EVEscape_compare_natural_ba2_ba5_xbb.html">Notebook comparing change in clade growth to change in phenotype</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/compare_natural/EVEscape_clade_pair_growth_ba2_ba5_xbb.csv">CSV with data for comparison of changes in growth vs phenotype for clade pairs</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/compare_natural/EVEscape_clade_growth_ba2_ba5_xbb.csv">CSV with phenotypes and growth for all individual clades</a></li>
</ul></details>
</li>
<li><details><summary>Comparison for EVEscape_components (BA.2, BA.5, and XBB clades) (click triangle to expand/collapse)</summary><ul>
<li><a href="htmls/EVEscape_components_clade_pair_growth_ba2_ba5_xbb.html">Correlation of change in clade growth versus phenotype for clade pairs</a></li>
<li><a href="htmls/EVEscape_components_ols_clade_pair_growth_ba2_ba5_xbb.html">OLS change in clade growth versus phenotype for clade pairs</a></li>
<li><a href="htmls/EVEscape_components_clade_growth_ba2_ba5_xbb.html">Correlation of absolute clade growth versus phenotype</a></li>
<li><a href="notebooks/EVEscape_components_compare_natural_ba2_ba5_xbb.html">Notebook comparing change in clade growth to change in phenotype</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/compare_natural/EVEscape_components_clade_pair_growth_ba2_ba5_xbb.csv">CSV with data for comparison of changes in growth vs phenotype for clade pairs</a></li>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS/blob/main/results/compare_natural/EVEscape_components_clade_growth_ba2_ba5_xbb.csv">CSV with phenotypes and growth for all individual clades</a></li>
</ul></details>
</li>
</ul>
<h4 id="comparison-of-growth-rates-estimated-by-murrell-and-bedford-groups">Comparison of growth rates estimated by Murrell and Bedford groups</h4>
<ul>
<li><a href="notebooks/compare_murrell_bedford_growth_rates.html">Notebook comparing Murrell and Bedford growth rates</a></li>
</ul>
<h4 id="comparison-to-ba286-evolution">Comparison to BA.2.86 evolution</h4>
<ul>
<li><a href="notebooks/compare_BA.2.86.html">Notebook comparing phenotypes to BA.2.86 evolution</a></li>
</ul>
<h4 id="escape-stratified-by-one-or-multiple-prior-infections">Escape stratified by one or multiple prior infections</h4>
<ul>
<li><a href="notebooks/escape_by_prior_infections.html">Notebook plotting escape with one versus multiple prior infections</a></li>
</ul>
<h4 id="analysis-of-mutational-effects-on-cell-entry">Analysis of mutational effects on cell entry</h4>
<ul>
<li><a href="htmls/strain_corr.html">Correlation of cell entry effects among strains</a></li>
<li><a href="htmls/natural_corr.html">Correlation with fitness effects estimated from natural sequences</a></li>
<li><a href="htmls/effects_boxplot.html">Distribution of cell entry effects</a></li>
<li><a href="htmls/key_mutations.html">Effects of key mutations on cell entry</a></li>
</ul>
<h4 id="ace2-binding-effects-of-non-rbd-mutations-in-natural-sequences">ACE2 binding effects of non-RBD mutations in natural sequences</h4>
<ul>
<li><a href="notebooks/non_rbd_binding_natural.html">Notebook analyzing ACE2 binding effects of non-RBD mutations in natural sequences</a></li>
</ul>
<h4 id="spike-site-numbering">Spike site numbering</h4>
<ul>
<li><a href="https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_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>