Analysis for "Comprehensive fitness landscape of AAV capsid reveals a viral gene and enables machine-guided design"

To get started make a virtual environment using the requirments.txt file provided

from inside the repo:

python3 -m venv venv
source venv/bin/activate
pip install -r requirments.txt

you should then be able to launch a jupyter notebook and run all analysis code as all data is provided within the repo

The code to process fastqs will require you download all fastqs from geo at this link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE139657