Metadata-Version: 2.1
Name: cy
Version: 0.1.6
Summary: Modelling CRISPR dropout data
Home-page: https://github.com/EmanuelGoncalves/crispy
Author: Emanuel Goncalves
Author-email: eg14@sanger.ac.uk
License: UNKNOWN
Description: ![Crispy logo](images/logo.png)
        
        [![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause) [![PyPI version](https://badge.fury.io/py/cy.svg)](https://badge.fury.io/py/cy)
        
        
        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
        import crispy as cy
        
        # Import data
        data = cy.get_example_data()
        
        # Association analysis
        crispy = cy.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])
        
        print(crispy)
        ```
        
        
        Install
        --
        
        ```
        pip install cy
        ```
        
        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: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Description-Content-Type: text/markdown
