Metadata-Version: 1.1
Name: cy
Version: 0.1.0.dev225
Summary: Crispy - modelling CRISPR dropout data
Home-page: https://github.com/EmanuelGoncalves/crispy
Author: Emanuel Goncalves
Author-email: eg14@sanger.ac.uk
License: BSD
Description: Crispy
        ============
        
        Identify associations between genomic alterations (e.g. structural variation, copy-number variation) and CRISPR-Cas9 knockout response.
        
        [Tandem duplications lead to loss of fitness effects in CRISPR-Cas9 data](https://www.biorxiv.org/content/early/2018/05/25/325076)
        
        
        Description
        --
        Crispy uses [Sklearn](http://scikit-learn.org/stable/index.html) implementation of [Gaussian Process Regression](http://scikit-learn.org/stable/modules/generated/sklearn.gaussian_process.GaussianProcessRegressor.html#sklearn.gaussian_process.GaussianProcessRegressor), fitting by default each chromosome of each sample independently.
        
        
        Example
        --
        ```python
        import pandas as pd
        from crispy.association import CRISPRCorrection
        
        # Import data
        data = pd.read_csv('extdata/association_example_data.csv', index_col=0)
        
        # Association analysis
        crispy = CRISPRCorrection()\
            .fit_by(by=data['chr'], X=data[['cnv']], y=data['fc'])
        
        # Export
        crispy = pd.concat([v.to_dataframe() for k, v in crispy.items()])\
            .sort_values(['cnv', 'k_mean'], ascending=[False, True])
        ```
        
        
        Install
        --
        
        ```
        python setup.py install
        ```
        
        Enrichment module has Cython files, to compile run:
        
        ```
        python crispy/enrichment/gsea_setup.py build_ext --inplace
        ```
        
        Regression module has Cython files, to compile run:
        
        ```
        python crispy/regression/linear_setup.py build_ext --inplace
        ```
        
        
Platform: UNKNOWN
Classifier: Development Status :: 1 - Planning
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
