Metadata-Version: 1.1
Name: iCount
Version: 2.0.0
Summary: Computational pipeline for analysis of iCLIP data
Home-page: https://github.com/tomazc/iCount
Author: University of Ljubljana, Bioinformatics Laboratory
Author-email: tomazc@gmail.com
License: MIT
Description: |Build Status| |PyPI version| |codecov| |Codacy Badge| |CLA assistant|
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        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.
        
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           :target: https://hub.docker.com/r/tomazc/icount/
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Keywords: iCLIP protein-RNA
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
