Name		Name	Last commit message	Last commit date
parent directory ..
data		data
plasmid_maps		plasmid_maps
results		results
README.md		README.md
config.yaml		config.yaml
depletion_neuts.ipynb		depletion_neuts.ipynb
escape_logoplots_for_key_sites.py.ipynb		escape_logoplots_for_key_sites.py.ipynb
rbd_depletions.ipynb		rbd_depletions.ipynb
validation_neuts.ipynb		validation_neuts.ipynb
virus_titers.ipynb		virus_titers.ipynb

README.md

These notebooks run manually outside of the pipeline

./virus_titers.ipynb/ notebook calculates pseudovirus titers.

./validation_neuts.ipynb/ notebook includes pseudovirus neutralization experiments for DMS validation.

./rbd_depletions.ipynb/ notebook plots ELISA binding curves for sera pre- and post- RBD-binding antibody depletions.

./depletion_neuts.ipynb/ notebook includes pseudovirus neutralization assays pre- and post- RBD-binding antibody depletion.

./escape_logoplots_for_key_sites.py.ipynb/ notebook plots logo plots at key escape sites

Results from all notebooks are in ./results.

./config.yaml/ contains data paths.

Plasmid maps for spike used for pseudotyping ./plasmid_maps.