Metadata-Version: 1.1
Name: intervene
Version: 0.6.5
Summary: A tool for intersection and visualization of multiple gene or genomic region sets
Home-page: https://github.com/asntech/intervene
Author: Aziz Khan
Author-email: azez.khan@gmail.com
License: MIT
Description: .. image:: https://raw.githubusercontent.com/asntech/intervene/master/docs/img/intervene_logo.png
           	:target: http://intervene.readthedocs.org
           	
        Intervene
        -----------
        
        	a tool for intersection and visualization of multiple gene or genomic region sets
        
        .. image:: https://travis-ci.org/asntech/intervene.svg?branch=master
            :target: https://travis-ci.org/asntech/intervene
        
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            :target: https://www.python.org
        
        .. image:: https://img.shields.io/pypi/v/intervene.svg
            :target: https://pypi.python.org/pypi/intervene
        
        .. image:: https://anaconda.org/bioconda/intervene/badges/version.svg
        	:target: https://anaconda.org/bioconda/intervene
        
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        	:target: https://conda.anaconda.org/bioconda
        
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        Documentation
        =============
        
        **A detailed documentation is available in different formats:**  `HTML <http://intervene.readthedocs.org>`_ | `PDF <http://readthedocs.org/projects/intervene/downloads/pdf/latest/>`_ | `ePUB <http://readthedocs.org/projects/intervene/downloads/epub/latest/>`_
        
        .. figure:: http://intervene.readthedocs.io/en/latest/_images/Intervene_sketch.png
           :width: 800px
           :align: left
        
        Installation
        ============
        
        Quick installation using Conda
        ------------------------------
        
        .. code-block:: bash
        
        	conda install -c bioconda intervene
        
        This will install all the dependencies and you are ready to use Intervene.
        
        Install using `pip`
        -------------------
        You can install Intervene from PyPi using pip.
        
        Install from PyPi::
        
        	pip install intervene
        
        Note: If you install using pip, make sure to install BEDTools and R packages listed below. 
        
        Intervene requires the following Python modules and R packages:
        
        	* Python (=> 3.3 ): https://www.python.org/
        	* BedTools (Latest version): https://github.com/arq5x/bedtools2
        	* pybedtools (>= 0.7.9): https://daler.github.io/pybedtools/
        	* Pandas (>= 0.16.0): http://pandas.pydata.org/
        	* Seaborn (>= 0.7.1): http://seaborn.pydata.org/
        	* R (>= 3.0): https://www.r-project.org/
        	* R packages including UpSetR (v1.4.0), corrplot
        
        Install BEDTools
        ----------------
        We are using pybedtools, which is Python wrapper for BEDTools. So, BEDTools should be installed before using Intervene. It's recomended to have a latest version, but if you have an older version already install, it should be fine.
        
        A quick installation, if you have conda installed.
        
        .. code-block:: bash
        
            conda install -c bioconda bedtools
        
        Please read the instructions at https://github.com/arq5x/bedtools2 to install BEDTools, and make sure it is on your path and you are able to call bedtools from any directory.
        
        
        Install required R packages
        ---------------------------
        
        Intervene rquires three R packages, `UpSetR <https://cran.r-project.org/package=UpSetR>`_ , `corrplot <https://cran.r-project.org/package=corrplot>`_ for visualization and `Cairo <https://cran.r-project.org/package=Cairo>`_ to generate high-quality vector and bitmap figures.
        
        .. code-block:: R
        
            install.packages(c("UpSetR", "corrplot", "Cairo"))
        
        Install Intervene from source
        =============================
        You can install a development version by using ``git`` from GitHub or Bitbucket.
        
        
        Install development version from `Bitbucket`
        --------------------------------------------
        
        If you have `git` installed, use this:
        
        .. code-block:: bash
        
            git clone https://bitbucket.org/CBGR/intervene.git
            cd intervene
            python setup.py sdist install
        
        Install development version from `GitHub`
        -----------------------------------------
        If you have `git` installed, use this:
        
        .. code-block:: bash
        
            git clone https://github.com/asntech/intervene.git
            cd intervene
            python setup.py sdist install
        
        How to use Intervene
        ====================
        Once you have installed Intervene, you can type:
        
        .. code-block:: bash
        
        	intervene --help
        
        This will show the following help message.
        
        .. code-block:: bash
        
        	usage: intervene <subcommand> [options]
        	    
        	positional arguments <subcommand>:
        	  {venn,upset,pairwise}
        	                        List of subcommands
        	    venn                Venn diagram of intersection of genomic regions or list sets (upto 6-way).
        	    upset               UpSet diagram of intersection of genomic regions or list sets.
        	    pairwise            Pairwise intersection and heatmap of N genomic region sets in <BED/GTF/GFF> format.
        
        	optional arguments:
        	  -h, --help            show this help message and exit
        	  -v, --version         show program's version number and exit
        
        
        to see the help for the three subcommands ``pairwise``, ``venn`` and ``upset`` type:
        
        .. code-block:: bash
        	
        	intervene pairwise --help
        
        	intervene venn --help
        
        	intervene upset --help
        
        Run Intervene on test data
        --------------------------
        
        To run Intervene using example data, use the following commands. To access the test data make sure you have ``sudo`` or ``root`` access.
        
        .. code-block:: bash
        
        	intervene pairwise --test
        
        	intervene venn --test
        
        	intervene upset --test
        
        If you have installed Intervene locally from the source code, you may have problem to find test data. You can download the test data here https://github.com/asntech/intervene/tree/master/intervene/example_data and point to it using ``-i`` instead of ``--test``.
        
        .. code-block:: bash
        
        	./intervene/intervene venn -i intervene/example_data/ENCODE_hESC/*.bed       
          	./intervene/intervene upset -i intervene/example_data/ENCODE_hESC/*.bed      
          	./intervene/intervene pairwise -i intervene/example_data/dbSUPER_mm9/*.bed  
        
        The above three test commands will generate the following three figures (a, b and c).
        
        .. figure:: http://intervene.readthedocs.io/en/latest/_images/Intervene_plots.png
           :width: 800px
           :align: left
        
        By default your results will stored in the current working directory with a folder named ``Intervene_results``. If you wish to save the results in a specific folder, you can type::
        
        	intervene upset --test --output ~/path/to/your/folder
        
        Interactive Shiny App
        =====================
        Intervene Shiny App is freely available at https://asntech.shinyapps.io/intervene or https://intervene.shinyapps.io/intervene
        
        The source code for the Shiny app is available at https://github.com/asntech/intervene-shiny
        
        Support
        ========
        If you have questions, or found any bug in the program, please write to us at ``aziz.khan[at]ncmm.uio.no``
        
        Cite Us
        =========
        If you use Intervene please cite us: ``Khan A, Mathelier A. Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. BMC Bioinformatics. 2017;18:287. doi: 10.1186/s12859-017-1708-7``
        
        
Platform: linux/unix
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
