README

This repository contains the majority of the code and data necessary to generate the bGWAS paper on C. difficile in vitro phenotypes. 

figures: Final paper figures.
data: Hogwash input and output data as well as data generated by post-hogwash analyses. Some data will be too large to share on github (either ZIP or make accessible upon request or host on an alternate server).
lib: All of the code needed to prep the input data, run hogwash, perform post-hogwash analyses, and generate plots for final figures.
notebook: Exploratory data analyses. 

Paper authors: Katie Saund, Ali Pirani, Evan Snitkin. Possibly: Phil Hanna, Borden Lacey.