Metadata-Version: 1.1
Name: runHiC
Version: 0.7.0-r2
Summary: A easy-to-use Hi-C processing software based on hiclib
Home-page: https://github.com/XiaoTaoWang/HiC_pipeline
Author: XiaoTao Wang
Author-email: wangxiaotao868@163.com
License: UNKNOWN
Description: runHiC
        ******
        .. image:: https://zenodo.org/badge/doi/10.5281/zenodo.55324.svg
           :target: http://dx.doi.org/10.5281/zenodo.55324
        
        runHiC is a easy-to-use Hi-C processing software based on hiclib (https://bitbucket.org/mirnylab/hiclib)
        Different from hiclib, which was born for flexibility, runHiC is a customized pipeline, and can be
        run from command line directly.
        
        Since version 0.7.0, runHiC has been able to execute concurrently either on a single laptop with multiple
        processors or on a PBS-based clusters.
        
        Design Concepts
        ===============
        runHiC is designed to process Hi-C data from raw sequencing reads(.sra, .fastq, .fastq.gz) to the corrected
        contact matrices. It separates the whole procedure into 4 stages(*mapping*, *filtering*, *binning*,
        *correcting*) and contains 7 subcommands:
        
        +------------+------------------------------------------------------------------------------+
        | mapping    | Iteratively map pair-end sequencing reads to a supplied genome               |
        +------------+------------------------------------------------------------------------------+
        | filtering  | Perform read-level and fragment-level noise removing                         |
        +------------+------------------------------------------------------------------------------+
        | binning    | Generate the original contact matrices                                       |
        +------------+------------------------------------------------------------------------------+
        | correcting | Perform iterative corrections on original contact matrices                   |
        +------------+------------------------------------------------------------------------------+
        | tosparse   | Convert the dense intra-chromosomal contact matrices to sparse ones          |
        +------------+------------------------------------------------------------------------------+
        | pileup     | Streamline all stages from *mapping* to *correcting*                         |
        +------------+------------------------------------------------------------------------------+
        | quality    | Assess the quality of your Hi-C data                                         |
        +------------+------------------------------------------------------------------------------+
        
        Links
        =====
        - `Detailed Documentation <http://xiaotaowang.github.io/HiC_pipeline/>`_
            - `Installation <http://xiaotaowang.github.io/HiC_pipeline/install.html>`_
            - `Quick Start <http://xiaotaowang.github.io/HiC_pipeline/quickstart.html>`_
            - `Data Quality <http://xiaotaowang.github.io/HiC_pipeline/quality.html>`_
            - `Parallel Computation <http://xiaotaowang.github.io/HiC_pipeline/parallel.html>`_
        - `Code Repository <https://github.com/XiaoTaoWang/HiC_pipeline/>`_ (At GitHub, Track the package issue)
        - `PyPI <https://pypi.python.org/pypi/runHiC>`_ (Download and Installation)
        
        Usage
        =====
        Open a terminal, type ``runHiC -h`` and ``runHiC <subcommand> -h`` for help information.
        
        Citation
        ========
        Xiaotao Wang. (2016). runHiC: A user-friendly Hi-C data processing software based on hiclib. Zenodo.
        `10.5281/zenodo.55324 <http://dx.doi.org/10.5281/zenodo.55324>`_
        
Keywords: Hi-C HiC ICE Contact
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
Classifier: Operating System :: POSIX
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
