# NucleoATAC

**This package is no longer being actively maintained; feel free to post issues that others in the community may respond to, but this package will likely not be updated further. Additionally, if anyone wants to maintain a fork of the package or has developed an alternative package for similar purposes, would be happy to link to that repo here.**

Python package for calling nucleosomes using ATAC-seq data.
Also includes general scripts for working with paired-end ATAC-seq data (or potentially other paired-end data).

Please cite our paper at [Genome Research](http://genome.cshlp.org/content/25/11/1757) if you use this tool in your research.

Please use GitHub Issues to bring up any errors that occur with software rather than emailing authors.

Note on Versions:  

* version 0 represents code used for biorxiv manuscript
* version 0.2.1 was used for Genome Research manuscript (See Supplemental Information as well)

Documentation  can be found at http://nucleoatac.readthedocs.org/en/latest/

If you want to easily read in NucleoATAC outputs into R for further processing or exploration, check out [NucleoATACR](https://github.com/GreenleafLab/NucleoATACR/)

Currently NucleoATAC only supports Python 2.7 (No Python 3). If anyone is interested in adding Python 3 support, pull requests welcome :smile: