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
Additional files
HA site numbering
Cell entry effect comparison
Functional effect distribution