Deep mutational scanning of HIV Envelope BF520 with anti-CD4 binding site sera and antibodies¶
This page documents the data analysis. For the actual code, see https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera
Study by Caelan Radford, Jesse Bloom, et al. See the pre-print here (https://www.biorxiv.org/content/10.1101/2023.03.23.533993v1).
Workflow¶
Below is the rulegraph for the snakemake workflow.
Click here
for the more detailed filegraph.
Analysis notebooks¶
Many of the plots in these notebooks are interactive, so try mousing over points for details, using dropdowns, etc.
- Analyze PacBio CCSs
- Build PacBio consensus sequences
- Build the codon variants
- Functional scores of variants for viral entry
- Fit global epistasis models
- Functional effects of mutations across replicates
- Counts of variants
- Probabilities of escape and neutralization in antibody selections
- Fit
polyclonal
models - Antibody-escape averaged across replicates
- Validation neutralization assays versus
polyclonal
fits - Mutation effects compared to natural sequence variation