Analysis by Dadonaite et al (2024)
See https://github.com/dms-vep/Flu_H5_American-Wigeon_South-Carolina_2021-H5N1_DMS for full code.
Barcode to codon-variant lookup table
Analysis notebooks
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)
Interactive plots of differences in functional effects between conditions (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)
Notebooks taking differences in functional effects between conditions (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)
Differences in functional 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)
stability
Final summary plots
stability mutation effect plots (click triangle to expand/collapse)
Analysis notebooks
Fits of polyclonal models to individual stability selections (click triangle to expand/collapse)
Average selections for stability (click triangle to expand/collapse)
Data files
Probability (fraction) escape for each variant in each stability selection (CSVs) (click triangle to expand/collapse)
stability CSVs (click triangle to expand/collapse)
Integrated summary plots
phenotypes
all sera escape
VRC antibody escape
mRNA vaccine mouse sera escape
cattle sera escape
Crowe antibody escape
Stabilized HA sera escape
Additional files
HA site numbering
Cell entry effect comparison
Functional effect distribution
Visualizations of DMS data on protein structure (dms-viz JSONs)