.. xpore documentation master file, created by
   sphinx-quickstart on Sat Dec 21 06:31:05 2019.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to xPore's documentation!
=================================
xPore is a Python package for identification of differentail RNA modifications from Nanopore sequencing data.

To install the latest release, run::

    pip install xpore

See our :ref:`Installation page <installation>` for details.

To check the version of xPore, run::

    xpore -v

To detect differential modifications, you can follow the instructions in our :ref:`Quickstart page <quickstart>`. 

Contents
------------------
.. toctree::
   :maxdepth: 1
   
   installation
   quickstart
   outputtable
   configuration
   preparation
   data
   cmd
   citing
   help

Contacts
--------
If you use xPore in your research, please cite

Ploy N. Pratanwanich, et al.,Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore. *Nat Biotechnol* (2021), `https://doi.org/10.1038/s41587-021-00949-w <https://doi.org/10.1038/s41587-021-00949-w>`_ 

xPore is maintained by `Ploy N. Pratanwanich <https://github.com/ploy-np>`_, `Yuk Kei Wan <https://github.com/yuukiiwa>`_ and `Jonathan Goeke <https://github.com/jonathangoeke>`_ from the Genome Institute of Singapore, A*STAR. 

If you want to contribute, please leave an issue in `our repo <https://github.com/GoekeLab/xpore>`_

Thank you!

