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Analyzes deep mutational scanning data. Enrich incorporates scoring methods applicable to deep mutational scans with any number of time points. It predicts variant scores and standard errors that mirror both sampling error and consistency between replicates. This software measures an enrichment ration to estimate fitness via the frequency of each variant before and after selection. It offers an alignment-free mode and an implementation of the Needleman-Wunsch global alignment algorithm to call insertion and deletion events.
A software package to infer the impacts of mutations from deep mutational scanning data using a likelihood-based treatment of the mutation counts. Using dms_tools, one can infer the preference of each site for each amino acid given a single selection pressure, or assess the extent to which these preferences change under different selection pressures. The preferences and their changes can be intuitively visualized with sequence-logo-style plots created using an extension to Weblogo.
dms2dfe / Deep Mutational Scanning data to Distribution of Fitness Effects
Provides utilities for downstream analysis such as identification of relative selection pressure, molecular constraints and visualizations of the data. dms2dfe is a tunable, open-source workflow that integrates state-of-the-art methods of genomics for analysis of deep mutational scanning (DMS) data. It implements noise reduction utilizing both sequencing depth and empirical Bayes shrinkage. This package also supports concatamer based approach as well as multiplexing strategy using barcoded amplicons.
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