Deep mutational scanning (DMS) pipeline for a viral entry protein (VEP)
Analysis by Jesse Bloom (2023)
See https://github.com/dms-vep/dms-vep-pipeline-3 for full code.
Documentation of results rendered as of Thu Nov 6 13:23:56 2025
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 functional effects from single-mutant variants only (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)
Interactive plots of average shifts in functional 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)
Notebooks taking differences in functional effects between conditions (click triangle to expand/collapse)
Notebooks fitting shifts in functional effects (click triangle to expand/collapse)
Notebooks averaging shifts in 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 functional effects from single-mutant variants only (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)
Per-condition functional effect shifts CSVs (click triangle to expand/collapse)
Average shifts 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)
Receptor affinity
Final summary plots
receptor affinity mutation effect plots (click triangle to expand/collapse)
Analysis notebooks
Fits of polyclonal models to individual receptor affinity selections (click triangle to expand/collapse)
Average selections for receptor affinity (click triangle to expand/collapse)
Data files
Probability (fraction) escape for each variant in each receptor affinity selection (CSVs) (click triangle to expand/collapse)
receptor affinity CSVs (click triangle to expand/collapse)
Integrated summary plots
summary of all phenotypes
summary of just antibodies
summary of just entry and binding
Additional analysis-specific files
Data files