Metadata-Version: 2.1
Name: gpseqc
Version: 2.3.6
Summary: GPSeq-based centrality estimation.
Home-page: https://github.com/ggirelli/gpseqc
Author: Gabriele Girelli
Author-email: gabriele.girelli@scilifelab.se
License: MIT
Description: gpseqc
        ===
        
        A Python3 package that provides tools to estimate the 3D spatial nuclear centrality of genomic regions and compare different centrality rankings.
        
        * Read the (public) [documentation](https://ggirelli.github.io/gpseqc/) for more details.
        * Read the (private) [documentation](https://github.com/ggirelli/gpseqc/wiki) for more details.  
        *Once the repo goes public, private docs will be merged with public ones.*
        
        Installation
        ---
        
        To **install**, run the following:
        
        ```
        git clone http://github.com/ggirelli/gpseqc
        cd gpseqc
        sudo -H pip3 install .
        ```
        
        To **test** your installation, run: `pytest-3 --pyargs gpseqc`.
        
        To **uninstall** run the following from within the repository folder:
        
        ```
        sudo -H pip3 uninstall gpseqc
        ```
        
        To **update**, first uninstall, and then run the following from within the repository folder.
        
        ```
        git pull
        sudo -H pip3 install .
        ```
        
        ### Additional dependencies
        
        Most of the required dependencies are automatically install by `pip3`. Still, some require some manual steps. Specifically, `gpseqc` requires the following packages:
        
        * `tkinter`
        
        That on Ubuntu can be easily installed with:
        
        ```bash
        sudo apt install python3-tk
        ```
        
        Usage
        ---
        
        #### Estimate centrality
        
        The `gpseqc_estimate` script allows to estimate regional nuclear centrality based on a multi-condition GPSeq experiment. Run `gpseqc_estimate -h` for more details.
        
        #### Compare centrality ranks
        
        The `gpseqc_compare` script allows to compare different regional centrality ranks. Run `gpseqc_compare -h` for more details.
        
        Contributing
        ---
        
        We welcome any contributions to `GPSeqC`. Please, refer to the [contribution guidelines](https://ggirelli.github.io/gpseqc/contributing) if this is your first time contributing! Also, check out our [code of conduct](https://ggirelli.github.io/gpseqc/code_of_conduct).
        
        License
        ---
        
        ```
        MIT License
        Copyright (c) 2017-18 Gabriele Girelli
        ```
        
Keywords: DNA biology cell centrality nucleus genome region bed
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3 :: Only
Description-Content-Type: text/markdown
