SARS-CoV-2 Spike multidms analysis

Analysis of SARS-CoV-2 spike homologs as seen in our manuscript Jointly modeling deep mutational scans identifies shifted mutational effects among SARS-CoV-2 spike homologs. Please see the web page to explore the analysis interactively.

This repository contains the code in the form of a jupyter notebook, as well as the source code for generating the page.

To run the notebook:

1. clone the repository

git clone https://github.com/matsengrp/SARS-CoV-2_spike_multidms.git

2. (recommended) create a new environment

mamba create --name multidms-spike python=3.11
mamba activate multidms-spike

2. install the requirements

pip install -r analysis_requirements.txt

3. run jupyter notebook

jupyter notebook

Key files

1. results/spike_analysis/mutations_df.csv contains the respective parameters and phenotype effects for all mutations analyzed in this study.
2. results/spike_analysis/training_functional_scores.csv contains the curated model training set of barcoded variants and their respective functional scores, for each of the two replicate.