iCount 2.0.0
Computational pipeline for analysis of iCLIP data
License: MIT
Keywords: iCLIP protein-RNA

|Build Status| |PyPI version| |codecov| |Codacy Badge| |CLA assistant|
|Docker Automated build| |Documentation Status|

iCount: protein-RNA interaction analysis
========================================

iCount is a Python module and associated command-line interface (CLI),
which provides all the commands needed to process iCLIP data on
protein-RNA interactions and generate:

-  demultiplexed and adapter-trimmed FASTQ files,
-  BAM files with mapped iCLIP reads,
-  identified protein-RNA cross-linked sites, saved to BED files,
-  peaks composed of statistically significant cross-linked sites, saved
   to BED files,
-  clusters of significant cross-linked sites, saved to BED files,
-  grouping of individual replicate experiments,
-  RNAmap generation showing the positional distribution of cross-linked
   sites relative to genomic landmarks,
-  kmer enrichment analysis,
-  and other.

You may start with the
`tutorial <http://icount.readthedocs.io/en/latest/tutorial.html>`__ or
dive into the
`documentation <http://icount.readthedocs.io/en/latest/index.html>`__.

Authors
-------

iCount is developed and supported by `Tomaž Curk <http://curk.info>`__
from the `Bioinformatics Laboratory <http://biolab.si>`__ at the
`University of Ljubljana <http://www.uni-lj.si>`__, `Faculty of Computer
and Information Science <http://www.fri.uni-lj.si>`__ and in
collaboration with the laboratory of `Jernej
Ule <http://ulelab.info>`__.

The development started in late 2008 when Tomaž Curk and Gregor Rot
wrote a first prototype of iCount. In mid-2016, `Jure
Zmrzlikar <https://github.com/JureZmrzlikar>`__ from
`Genialis <http://www.genialis.com>`__ helped refactoring and improving
the code, which is now available here. For details and full
acknowledgments, see the `how to
cite <http://icount.readthedocs.io/en/latest/cite.html>`__ section in
the documentation.

Contributing
------------

Contributions (pull requests) are welcome! Please submit your
contributions by following the
`guidelines <http://icount.readthedocs.io/en/latest/contributing.html>`__.

Reporting problems
------------------

Use the `issues page <https://github.com/tomazc/iCount/issues>`__ to
report issues and request enhancements. Before submitting, please check
the list of already reported issues. Also, have a look at the
`FAQ <http://icount.readthedocs.io/en/latest/faq.html>`__ to see if the
problem has been addressed already.

.. |Build Status| image:: https://travis-ci.org/tomazc/iCount.svg?branch=master
   :target: https://travis-ci.org/tomazc/iCount
.. |PyPI version| image:: https://badge.fury.io/py/iCount.svg
   :target: https://badge.fury.io/py/iCount
.. |codecov| image:: https://codecov.io/gh/tomazc/iCount/branch/master/graph/badge.svg?token=JhUJ66rnJ3
   :target: https://codecov.io/gh/tomazc/iCount
.. |Codacy Badge| image:: https://api.codacy.com/project/badge/Grade/b77d104b59a74946bf8905f82dd381e4
   :target: https://www.codacy.com/app/tomazc/iCount?utm_source=github.com&utm_medium=referral&utm_content=tomazc/iCount&utm_campaign=Badge_Grade
.. |CLA assistant| image:: https://cla-assistant.io/readme/badge/tomazc/iCount
   :target: https://cla-assistant.io/tomazc/iCount
.. |Docker Automated build| image:: https://img.shields.io/docker/automated/jrottenberg/ffmpeg.svg
   :target: https://hub.docker.com/r/tomazc/icount/
.. |Documentation Status| image:: https://readthedocs.org/projects/icount/badge/?version=latest
   :target: http://icount.readthedocs.io/en/latest/?badge=latest