Deep mutational scanning using HIV Envelopes BF520 and TRO11 to identify mutations that escape neutralization by antibodies 3BNC117 and 10-1074
Analysis by Caelan Radford and Jesse Bloom. See the pre-print here (https://www.biorxiv.org/content/10.1101/2025.01.30.635715v1) (2025)
See https://github.com/dms-vep/HIV_Envelope_BF520_DMS_3BNC117_10-1074/ for full code.
Barcode to codon-variant lookup table
Data files
Count barcodes for variants
Analysis notebooks
Data files
Barcode count CSVs (click triangle to expand/collapse)
Functional effects of mutations
Final summary plots
Interactive plots of average mutation functional effects (click triangle to expand/collapse)
Interactive plots of average mutation latent-phenotype effects (click triangle to expand/collapse)
Analysis notebooks
- Analysis of functional scores
Notebooks with per-selection global epistasis fitting (click triangle to expand/collapse)
Notebooks averaging mutation functional effects (click triangle to expand/collapse)
Data files
Per-variant functional score CSVs (click triangle to expand/collapse)
Per-selection mutation functional effect CSVs (click triangle to expand/collapse)
Average mutation functional effects (CSV files) (click triangle to expand/collapse)
Average mutation latent-phenotype effects (CSV files) (click triangle to expand/collapse)
Antibody/serum escape
Final summary plots
antibody escape mutation effect plots (click triangle to expand/collapse)
Analysis notebooks
Fits of polyclonal models to individual antibody escape selections (click triangle to expand/collapse)
Average selections for antibody escape (click triangle to expand/collapse)
Data files
Probability (fraction) escape for each variant in each antibody escape selection (CSVs) (click triangle to expand/collapse)
antibody escape CSVs (click triangle to expand/collapse)
Integrated summary plots
all antibodies
Additional analysis-specific files