Metadata-Version: 1.0
Name: scConnect
Version: 1.0.2
Summary: scConnect integrate gene expression profiles in scRNA-seq datasets with ligand and receptor interaction information from Guide to pharmacology to construct a graph containing all putative interaction between cell types in the dataset.
Home-page: UNKNOWN
Author: Jon E.T. Jakobsson
Author-email: jon.jakobsson@neuro.uu.se
License: License :: OSI Approved :: MIT License
Description: .. image:: https://readthedocs.org/projects/scconnect/badge/?version=latest
            :target: https://scconnect.readthedocs.io/en/latest/?badge=latest
            :alt: Documentation Status
         
        .. image:: https://travis-ci.com/JonETJakobsson/scConnect.svg?branch=master
            :target: https://travis-ci.com/JonETJakobsson/scConnect
            
        .. image:: https://badge.fury.io/py/scConnect.svg
            :target: https://badge.fury.io/py/scConnect
        
        .. image:: scConnect/assets/logo.png
          :width: 100px
          :align: center
          :height: 100px
         
        scConnect integrate gene expression profiles in scRNA-seq datasets with ligand and receptor interaction information from `Guide to pharmacology <https://www.guidetopharmacology.org/>`__ to construct a graph containing all putative interaction between cell types in the dataset. scConnect integrate well with Scanpy and  can be appended to  any scanpy analysis pipeline.
        
        =========
        Usecases:
        =========
        
        * Identify putative cell-cell communication in a tissue
        * Infer neuronal networks based on ligand receptor compatability
        * Study connectivity changes following treatment
        
        
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        Documentation and tutorial
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        For a short introduction to how scConnect can be used please check out this `tutorial`_ and for information about the API please consult the `documentation`_.
        
        The quickest and easiest way to try out the tutorial is to run through this binder:
        
        .. image:: https://mybinder.org/badge_logo.svg
         :target: https://mybinder.org/v2/gh/JonETJakobsson/scConnect/master?filepath=tutorial%2FConnecting%20brain%20regions.ipynb   
         
        .. _tutorial: https://github.com/JonETJakobsson/scConnect/blob/master/tutorial/Connecting%20brain%20regions.ipynb
        .. _documentation: https://scconnect.readthedocs.io/en/latest/
        
        
        
        
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        Installation
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        To install the latest stable version install using PYPI
        
        .. code-block:: bash
        
            pip install scConnect
            
        This will install all dependencies needed to run the tutorial, and utilize all features of scConnect.
        
        To install the master branch, please clone this repository and install using
        
        .. code-block:: bash
        
          cd scConnect/
          pip install .
          
          
        or
         
        .. code-block:: bash
         
           pip install git+https://github.com/JonETJakobsson/scConnect
            
        
        
        
          
        
        ===========
        Change log:
        ===========
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        1.0.2
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        * Fixed documentation issues (added .readthedocs.yml)
        * removed requirement.txt, build is constructed entirely from setup.py
        
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        1.0.1
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        Bugfixes:
        
        * Fixed a bug in connect.py which cased a crash when connecting ligands and receptors.
        
        
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        1.0.0
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        Initial release.
        
Platform: UNKNOWN
