Overview

This page contains a single notebook with all code used to produce the analysis in our manuscript: Jointly modeling deep mutational scans identifies shifted mutational effects among SARS-CoV-2 spike homologs. The purpose of this is two-fold: for code availability and reproducibility of our manuscript analysis, and as an example of how the multidms API might be used in your own analysis.

The source code for this page, key data files, as well as the relevant instructions to run the analysis yourself, can be found at https://github.com/matsengrp/SARS-CoV-2_spike_multidms

• Spike Analysis
  • Computational platform environment
  • Input Data
  • Variant barcode and mutation background stats
  • Encode data for fitting
  • Fit Models (Shrinkage Analysis)
  • Model Evaluation and Selection
  • Cross Validation
  • Global epistasis fits
  • Shifted mutations (interactive altair chart)
  • Shifted mutations (manually queried)
  • Comparison of results to the naive approach (independent-condition fits)
  • Comparison to linear model
  • Validation mutations
  • Model-reference choice comparison
  • Cumulative distribution of model sparsity
  • Correlation of BA2 and Delta Shifts
  • Structural Analysis