Metadata-Version: 2.1
Name: deepDegron
Version: 1.0.0
Summary: deepDegron
Home-page: https://github.com/ctokheim/deepDegron
Author: Collin Tokheim
Author-email: fake@gmail.com
License: Apache License, Version 2.0
Description: # deepDegron
        
        While a few UPS substrate mutations can be implicated in cancer based on known degrons, systematic investigation requires better degron annotation. To address this challenge, we developed a protein sequence-based model, deepDegron, that leverages data from the recently published high throughput global protein stability (GPS, (Koren et al., 2018; Timms et al., 2019)) assay of the n-terminal and c-terminal proteome to predict degrons. GPS measures the protein stability impact of peptides when attached to proteins (Yen et al., 2008), as measured by FACS-sorting of cells based on a fluorescent reporter protein (GFP, green) compared to a control reporter with no peptide attached (dsRed, red). Because the peptides consisted of known sequences and could contain degrons, deepDegron can learn sequence-rules of degron impact on protein stability.  
        
        [![Build Status](https://travis-ci.org/ctokheim/deepDegron.svg?branch=master)](https://travis-ci.org/ctokheim/deepDegron)
        
        ## Documentation
        
        For more documentation, please visit our [website documentation](https://deepdegron.readthedocs.io/en/latest/index.html).
        
        ## Installation 
        
        We recommend that you use python 3.7 to run deepDegron. 
        
        ### pip
        
        The easiest way to install deepDegron is through [pip](https://pip.pypa.io/en/stable/).
        
        ```bash
        $ pip install deepDegron
        ```
        
        ### From source
        
        As a first step, please change to the top-level directory in the deepDegron source code.
        
        You can install the dependencies of deepDegron using [conda](https://docs.conda.io/en/latest/). Once you have conda installed, create an environment to run deep degron using the following commands:
        
        ```bash
        $ conda env create -f environment.yml  # install dependencies
        $ source activate deepDegron  # activate environment
        $ pyensembl install --release 75 --species human  # download human reference data
        $ python setup.py install  # install deepDegron
        ```
        
        An alternative way to install the python dependencies is to use pip.
        
        ```bash
        $ python -m pip install --upgrade pip
        $ pip install -r requirements.txt  # install required packages
        $ pyensembl install --release 75 --species human  # download human reference data
        $ python setup.py install  # install deepDegron
        ```
        
Platform: UNKNOWN
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Description-Content-Type: text/markdown
