Exploration, clustering, visualization and classification of DNA damage patterns
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README.md

aRchaic

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

Structure Plot

Authors

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

**co-first authors

Installation

First and foremost, the user is required to install

And Python packages,

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

Upon completion of these steps, start a new R session and install the R dependency libraries.

install.packages("devtools")
devtools::install_github("kkdey/CountClust")
devtools::install_github("TaddyLab/maptpx")

aRchaic requires the package Logolas for visualization.

If you are using R version (>=3.4), you can install Logolas from Github.

devtools::install_github("kkdey/Logolas")

If you are using R version (>=3.5), you may install Logolas from Bioconductor as well.

source("https://bioconductor.org/biocLite.R")
biocLite("Logolas")

On completion of the above steps, install the R package aRchaic

devtools::install_github("kkdey/aRchaic")

Finally, load aRchaic into R

library(aRchaic)

Tutorial

Get started with a short tutorial here

Support

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

Citation

TBA

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.