Metadata-Version: 1.1
Name: netcoloc
Version: 0.1.7a1
Summary: UNKNOWN
Home-page: https://github.com/ucsd-ccbb/netcoloc
Author: Brin Rosenthal, Sophie Liu
Author-email: sbrosenthal@health.ucsd.edu, sol015@ucsd.edu
License: MIT license
Description: ===============================
        NetColoc
        ===============================
        
        .. image:: https://img.shields.io/pypi/v/netcoloc.svg
                :target: https://pypi.python.org/pypi/netcoloc
        
        .. image:: https://img.shields.io/travis/ceofy/netcoloc.svg
                :target: https://travis-ci.org/ceofy/netcoloc
        
        .. image:: https://readthedocs.org/projects/netcoloc/badge/?version=latest
                :target: https://netcoloc.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
                
        .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.6654561.svg
           :target: https://doi.org/10.5281/zenodo.6654561
        
        
        Description
        -----------
        
        Here we introduce NetColoc, a tool which evaluates the extent to
        which two gene sets are related in network space, i.e. the extent
        to which they are colocalized in a molecular interaction network,
        and interrogates the underlying biological pathways and processes
        using multiscale community detection.
        
        This framework may be applied to any number of scenarios in which
        gene sets have been associated with a phenotype or condition,
        including rare and common variants within the same disease,
        genes associated with two comorbid diseases, genetically
        correlated GWAS phenotypes, GWAS across two different species,
        or gene expression changes after treatment with two different
        drugs, to name a few.
        
        NetColoc relies on a dual network propagation
        approach to identify the region of network space which is
        significantly proximal to both input gene sets, and as such is
        highly effective for small to medium input gene sets.
        
        
        Documentation
        -------------
        
        For a quick-start on NetColoc's functionality, please see the
        `example notebooks <https://github.com/ucsd-ccbb/NetColoc/tree/main/example_notebooks>`__.  
        
        **Usage Note:** Please follow steps in example notebooks for correct usage of NetColoc. At this time, individual functionalities have not been tested for independent use. 
        
        Dependencies
        --------------
        
        NetColoc requires the following python packages:
        
        .. note:: All of the following packages minus `DDOT <https://github.com/idekerlab/ddot>`__ and `cdapsutil <https://pypi.org/project/cdapsutil>`__ will be automatically installed via ``pip install netcoloc``
        
        * `click <https://pypi.org/project/click>`__
        * `matplotlib <https://pypi.org/project/matplotlib>`__
        * `ndex2 <https://pypi.org/project/ndex2>`__
        * `networkx <https://pypi.org/project/networkx>`__
        * `numpy <https://pypi.org/project/numpy>`__
        * `seaborn <https://pypi.org/project/seaborn>`__
        * `tqdm <https://pypi.org/project/tqdm>`__
        * `mygene >= 3.2.2 <https://pypi.org/project/mygene/>`__
        * `scipy >= 1.5.3 <https://pypi.org/project/scipy/>`__
        * `statsmodels <https://pypi.org/project/statsmodels/>`__
        * `gprofiler-official >= 1.0.0 <https://pypi.org/project/gprofiler-official/>`__
        * `ipywidgets <https://pypi.org/project/ipywidgets>`__
        * `ipycytoscape <https://ipycytoscape.readthedocs.io/en/latest>`__
        
        * `python3 branch of DDOT <https://github.com/idekerlab/ddot/tree/python3>`__
        
          `DDOT <https://github.com/idekerlab/ddot>`__ can be installed one of
          two ways:
        
          1. To install `DDOT <https://github.com/idekerlab/ddot>`__ by downloading
             the zip file of the source tree:
        
             .. code-block::
        
                wget https://github.com/idekerlab/ddot/archive/refs/heads/python3.zip
                unzip python3.zip
                cd ddot-python3
                python setup.py bdist_wheel
                pip install dist/ddot*py3*whl
        
          2. To install `DDOT <https://github.com/idekerlab/ddot>`__ by cloning the repo:
        
             .. code-block::
        
                git clone --branch python3 https://github.com/idekerlab/ddot.git
                cd ddot
                python setup.py bdist_wheel
                pip install dist/ddot*py3*whl
        
          .. note::
            Due to dependency issue DDOT, will not work with Python 3.10 or later
        
        
        Additional requirements for full functionality of example notebook:
        
        * `cdapsutil >= 0.2.0a1 <https://pypi.org/project/cdapsutil/>`__
        
        
        Installation
        --------------
        
        NetColoc is available on `PyPI <https://pypi.org/>`__
        
        ::
        
             pip install netcoloc
        
        License
        --------
        
        * Free software: MIT license
        
        Citing NetColoc
        ---------------
        
        Coming soon...
        
        Credits
        -------
        
        This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
        
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
        
        
        =======
        History
        =======
        
        0.1.7 (2022-06-28)
        --------------------
        
        * Removed unused `network_localization.py` module
        
        0.1.6 (2022-06-16)
        --------------------
        
        * `ipycytoscape <https://ipycytoscape.readthedocs.io/en/latest>`__ added as a dependency
        
        * `ipywidgets <https://ipywidgets.readthedocs.io/en/latest>`__ added as a dependency
        
        * Added `network_colocalization.sweep_input_pvals()` to sweep p-values and scores
        
        * Added `network_colocalization.calculate_network_enrichment()` to sweep over z-score thresholds
        
        * `netprop.get_individual_heats_matrix()` can take a networkx `Graph` object and internally call
          `netprop.get_normalized_adjancency_matrix()`. Documentation updated in both methods to note
          that the resulting matrices can be saved via `numpy.save()` and retrieved via `numpy.load()`
        
        * `example_notebooks/ASD_CHD_NetColoc_analysis.ipynb` now visualizes hierarchy using
          `ipycytoscape <https://ipycytoscape.readthedocs.io/en/latest>`__
        
        * `example_notebooks/ASD_CHD_NetColoc_analysis.ipynb` updated with a note about using `numpy.save()`
          and `numpy.load()` to save and retrieve result from `netprop.get_individual_heats_matrix()`
          
        
        
        
        
        0.1.5 (2022-03-09)
        --------------------
        
        * Fixed divide by zero error seen when calculating cosine distance by updating `netprop.get_normalized_adjancency_matrix()`
          to properly normalize an adjacency matrix that is asymetric (UD-1863)
        
        0.1.4 (2021-08-31)
        --------------------
        
        * If import of DDOT package fails, only a warning message will be
          displayed unless user invokes ``netcoloc.validation.load_MPO()``
          in which case an ``ImportError`` is raised
        
        * Fixed bug where ``z1_threshold`` parameter was being passed to ``z2_threshold`` parameter in
          ``netcoloc.network_cololcalization.calcualte_network_overlap`` method called by ``netcoloc.network_colocalization.calculate_network_overlap_subgraph`` method
        
        0.1.3 (2021-08-18)
        --------------------
        
        * Added dependency `gprofiler-official <https://pypi.org/project/gprofiler-official>`__
          to ``setup.py`` and ``requirements.txt`` because this is used by
          ``network_colocalization.py``
        
        0.1.2 (2021-08-17)
        --------------------
        
        * Added new `validation.py` module containing mouse knockout database
          functionality
        
        0.1.1 (2021-08-06)
        -------------------
        
        * Fixed netcoloc imports in `netprop_zcore.py`
        
        
        0.1.0 (2021-03-10)
        ------------------
        
        * First release on PyPI.
        
Keywords: netcoloc
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
