Examples

The dms_variants package is designed to aid in the analysis of deep mutational scanning of barcoded variants of genes. It contains many Python functions and classes that you can use in scripts or Jupyter notebooks. Major functionality includes:

• The dms_variants.codonvarianttable.CodonVariantTable class for managing and analyze libraries of barcoded codon variants of genes.

• The dms_variants.illuminabarcodeparser.IlluminaBarcodeParser for easily parsing Illumina barcode sequencing that counts variants.

• The dms_variants.globalepistasis module for fitting global epistasis models to experiments on variants with multiple mutations.

Below are a series of examples that illustrate usage of this functionality and other aspects of the dms_variants package.

• Analyze simulated library of codon variants
• Variants with deletion mutations
• Libraries with secondary target genes
• Compute probabilities of escape
• Parse barcodes
• Fitting gobal epistasis models with experimental “noise”
• Formatting CodonVariantTable plots

The above examples can be run as interactive Jupyter notebooks on mybinder by going to the following link (it may take a minute to load) and then opening the notebook you want to run.