Deep mutational scanning (DMS) pipeline for a viral entry protein (VEP)

This page documents the data analysis. For the actual code, see https://github.com/dms-vep/dms-vep-pipeline

Study by Jesse Bloom.

Analysis notebooks

Many of the plots in these notebooks are interactive, so try mousing over points for details, using dropdowns, etc.

• Analyze PacBio CCSs
• Build PacBio consensus sequences
• Build the codon variants
• Functional scores of variants for viral entry
• Fit global epistasis models
• Functional effects of mutations across replicates
• Counts of variants
• Probabilities of escape and neutralization in antibody selections
• Fit polyclonal models
• Antibody-escape averaged across replicates

Data files

• parental gene sequence

• parental protein sequence

• sequential-to-reference site numbers

• codon-variant table

• processed barcode sequencing runs

• variant counts

• functional selection experiments

• mutation effects for each functional selection

• mutation functional effects replicate average (observed phenotype)

• mutation functional effects replicate average (latent phenotype)

• antibody selection experiments

• antibody escape values

Interactive plots of mutation functional effects

• Observed phenotype effects

• Latent phenotype effects

Interactive plots of mutation antibody escape

• REGN10933 escape plot

• REGN10933 icXX plot

• S2M11 escape plot

• S2M11 icXX plot