This repository contains code generated, and corresponding raw data, for 2016 Mouw et al, Genomic Evolution After Chemoradiotherapy in Anal Squamous Cell Carcinoma. This paper is available (http://clincancerres.aacrjournals.org/content/early/2017/03/14/1078-0432.CCR-16-2017.full-text.pdf)
All figures and statistics created for the paper are shown in ASCC-ipython_master.ipynb
Python 2.7 was primarily used for all data manipulation, calculations, and figure generation. The best way to acquire all packages used may be to download Anaconda. Specific python packages used are commented at the top of ASCC-ipython_master.ipynb
Due to file size constraints, we were unable to upload the proper version of "cosmic_v75.txt" and "exac_GATK.txt" (located under storage/reference/) to this repository. Please run ASCC-get_db.sh to download these two files off of dropbox.
After forking or downloading the repository, update these two files by:
bash ASCC-get_db.shPlease click here to contact us if you have any questions, comments, or concerns about this repository.
Please contact a corresponding author for any questions, comments, or concerns regarding the paper in general.