This repository contains the following data directories:
- Fitnesses: Individual fitness estimates for each of ~250,000 independent strains examined in screens carried out for this manuscript
- FitnessReports: Summaries of replicate fitness observations for each of ~25,000 different genotypes examined in these screens
- GISReports: Genetic interaction strength estimates generated by comparing fitness in matched pairs of QFA screens, as used in our online interactive plotting tool DIXY, for example. This directory also contains lists of genes that have been stripped from GIS analysis, together with the reason for their removal.
For detailed description of how to interpret columns and how fitnesses and genetic interaction strengths are calculated, please see the documentation for the R package which was used to generate them.
This directory contains a shiny app for interactive exploration of the QFA fitness profiles found in the FitnessReports directory above. If you would like to use profilyzer to explore your own data, please use the more general and updated version here.
Above is a static version of a plot that can be produced by profilyzer.
To see profilyzer in action, a live instance of this particular dataset can be found at this page. Alternatively, you can download the code & data from this repository and run a local session.
To run profilyzer in a local session:
- Check out this repository
- Open R session and set the current working directory to the one just above the profilyzer directory
- Ensure that you have shiny installed. If you do not, then execute the following in the R terminal:
install.packages("shiny") - Load the shiny library by executing the following in the R terminal:
library("shiny") - Finally, use profilyzer to browse the included LydallLab dataset:
runApp("profilyzer")