Metadata-Version: 2.1
Name: pymodulon
Version: 0.1.0
Summary: Python package for analyzing and visualizing iModulons.
Home-page: https://github.com/SBRG/pymodulon
Author: Anand V. Sastry
Author-email: avsastry@eng.ucsd.edu
Maintainer: Anand V. Sastry
Maintainer-email: avsastry@eng.ucsd.edu
License: MIT
Download-URL: https://pypi.org/project/pymodulon/
Project-URL: Source, https://github.com/SBRG/pymodulon
Project-URL: Tracker, https://github.com/SBRG/pymodulon/issues/
Description: **PyModulon** - Python package for analyzing and visualizing iModulons
        ======================================================================
        
        |PyPI|
        
        What is an iModulon?
        ~~~~~~~~~~~~~~~~~~~~
        To learn about iModulons, how they are computed, and what they can tell you, see our `about page <https://imodulondb.org/about.html>`_.
        
        Installation
        ~~~~~~~~~~~~
        
        Since **PyModulon** is currently under development, the recommended method to
        install **PyModulon** is to use the editable ``pip`` installation. It is
        recommended to do this inside a `virtual environment
        <http://docs.python-guide.org/en/latest/dev/virtualenvs/>`_ or in a `conda
        environment <https://docs.conda.io/en/latest/>`_. This is because we require
        Python 3.8 for certain functionalities.
        
        To create the conda environment::
        
        	conda create -n pymodulon python=3.8
        	conda activate pymodulon
        
        (Optional) Install other dependencies::
        
        	conda install -c anaconda graphviz
        	conda install -c bioconda meme blast
        
        Next, download the github repository::
        
        	git clone https://github.com/SBRG/pymodulon.git
        
        Then install with ``pip`` using the ``-e`` flag::
        
        	python -m pip install -e .
        
        This method of installation will automatically update your
        package each time you pull from this repository.
        
        To update your code, run the following from your local **PyModulon** folder::
        
        	git pull
        
        .. The recommended method is to install **PyModulon** is to use ``pip`` to
        .. `install pymodulon from PyPI <https://pypi.python.org/pypi/pymodulon>`_. It is
        .. recommended to do this inside a `virtual environment
        .. <http://docs.python-guide.org/en/latest/dev/virtualenvs/>`_)::
        
        .. 	pip install pymodulon
        
        .. in the ``pymodulon`` source directory. For additional information, please refer to the
        .. the `detailed installation instructions <INSTALL.rst>`_.
        
        Documentation
        -------------
        The documentation for **PyModulon** can be found `here <http://pymodulon.readthedocs.io/>`_.
        
        Development
        -----------
        If you would like to assist in development, please install `pre-commit <https://pre-commit.com/>`_ to ensure code style and consistency.
        
        Cite
        ----
        Please cite the original *E. coli* iModulon paper: `Sastry et al. Nature Communications. 2019. <https://www.nature.com/articles/s41467-019-13483-w>`_
        
        If you use organism-specific datasets in your work, please cite these datasets:
        
        * *Escherichia coli*: `Sastry et al. Nature Communications. 2019. <https://www.nature.com/articles/s41467-019-13483-w>`_
        * *Bacillus subtilis*: `Rychel et al. Nature Communications. 2020.  <https://www.nature.com/articles/s41467-020-20153-9>`_
        * *Staphylococcus aureus*: `Poudel et al. PNAS. 2020. <https://www.pnas.org/content/117/29/17228.abstract>`_
        
        .. |PyPI| image:: https://badge.fury.io/py/pymodulon.svg
            :target: https://pypi.python.org/pypi/pymodulon
        
Keywords: python,iModulon,RNA-seq,transcriptomics,ICA,regulation
Platform: GNU/Linux
Platform: Mac OS X > 10.7
Platform: Microsoft Windows >= 7
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/x-rst
Provides-Extra: dev
Provides-Extra: docs
Provides-Extra: tests
Provides-Extra: all
