Analysis by Carr, Crawford, ..., Bloom (2023)
See https://github.com/dms-vep/LASV_Josiah_GP_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 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 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 latent-phenotype 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)
Integrated summary plots
phenotypes
Additional analyses and data files
Variant mutation analysis
Correlations of DAG1 ortholog functional selections
Functional and antibody selection validations
Functional scores for different GPC regions
Comparisons of natural Lassa GPC diveristy to DMS data
Filtered antibody escape and functional data
Antibody escape compared to functional effects
Mapped data onto pdb structure