To encourage transparency, replicability/reproducibility, and also for educational purposes, the scripts herein replicate the major figures and findings associated with the following publication:
http://jamanetwork.com/journals/jamaoncology/article-abstract/2588642
Note that there may be aesthetic or minor differences in figures that are published. If you are interested in other information/scripts/data absent in this repository or the publication, including supplements -- please contact the authors directly. Data/scripts reproducing figures involving raw sequencing data are not included in this repository, and will instead be deposited in more appropriate, controlled access databases (i.e. dbGap) whenever possible.
To reproduce a publication:
1) Download directory for publication of interest from github
2) Run installRequiredPackages.R to install necessary R packages from CRAN and Bioconductor
3) Modify line 3 of [publication].R script to set publication directory on your local machine as userDirectory
4) Run [publication].R script to produce figures in dataOutput directory
Good luck...!