aRchaic

An R package for exploration, clustering and visualization of DNA damage patterns.

Authors

Kushal K Dey*, Hussein Al-Asadi *, John Novembre, Matthew Stephens

Installation

First and foremost, the user is required to install

• python
• R/RStudio

And Python packages,

• pysam
• pyfaidx

aRchaic requires R version to be 3.4 or greater. If your R version is lower than that, please upgrade.

Upon completion of these steps, start a new R session and install aRchaic:

install.packages("remotes")
remotes::install_github("kkdey/aRchaic")

Now you should be able to load aRchaic into R.

library(aRchaic)

Tutorial

Get started with a short tutorial here

Support

• Create a new issue to report bugs and/or request features.
• Contact Kushal Dey (kkdey@uchicago.edu) or Hussein Al-Asadi (halasadi@uchicago.edu)

Also users are welcome to contribute to the package by submitting pull request.

Citation

Al-Asadi, H., Dey, K., Novembre, J. and Stephens, M., 2018. Inference and visualization of DNA damage patterns using a grade of membership model. bioRxiv, p.327684.

License

Distributed under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

The repository is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. Please see LICENSE for more details.

Acknowledgements

The authors would like to acknowledge Anna Di Rienzo, Choongwon Jeong, Anna Gosling, John Lindo, David Witonsky, Joseph Marcus, John Blischak, Peter Carbonetto and members of Stephens Lab and Novembre Lab for helpful discussions.