Retron Library Recombineering Maintained by Max Schubert [email protected] and Daniel Goodman [email protected] .
This repository contains all scripts used to generate results for this publication, and the processed data required to run these scripts.
The Majority of figures are generated in R, and rMarkdown(.rmd) files are given for each figure or figure panel. In some cases one rMarkdown file is used to generate several figure panels. Scripts within these files retreive data from folders within this repository, generally organized by the figure to which they pertain.
Population simulations and simulations of editing are performed in Matlab, giving rise to images in supplemental figure 5. These scripts can be found in supplemental_figures/fig_s5
Alignment and calculation of coverage depth in figures 5B, 5C, and S9B, as well as deriving the "template lengths" depicted in S9A, are performed as described in the Online Methods section. Clarification and example scripting commands are available upon reasonable request.
Documentation, Code, and Figures for High throughput functional variant screens via in-vivo production of single-stranded DNA.