dms_variants package

dms_variants

Python package for analyzing deep mutational scanning of barcoded variants of genes.

Submodules

• barcodes
• bottlenecks
• codonvarianttable
• constants
• fastq
• globalepistasis
  • Global epistasis function
    • No epistasis function
    • Monotonic spline epistasis function
    • Multiple latent phenotypes
  • Likelihood calculation
    • Gaussian likelihood
    • Cauchy likelihood
    • Bottleneck likelihood
  • The model classes
  • Details of fitting
    • Fitting workflow
    • Fitting multiple latent phenotypes
    • Conveniently fitting and comparing several models
    • Vector representation of \(\beta_{\rm{wt}}\)
    • Optimization
    • Gradients used in optimization
  • Detailed documentation of models
• illuminabarcodeparser
• ispline
• pdb_utils
• plotnine_themes
• simulate
• utils