Metadata-Version: 1.2
Name: gnt
Version: 0.3.1
Summary: Python packcage for caidentifying Genetic iNTeractions from combinatorial screening data.
Home-page: https://github.com/gpp-rnd/gnt
Author: Peter C. DeWeirdt
Author-email: petedeweirdt@gmail.com
License: MIT license
Description: ===
        gnt
        ===
        
        
        .. image:: https://img.shields.io/pypi/v/gnt.svg
                :target: https://pypi.python.org/pypi/gnt
        
        .. image:: https://api.travis-ci.com/gpp-rnd/gnt.svg
                :target: https://travis-ci.com/gpp-rnd/gnt
        
        .. image:: https://readthedocs.org/projects/gnt/badge/?version=latest
                :target: https://gnt.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
        
        
        
        Python package for identifying Genetic iNTeractions from combinatorial screening data.
        
        
        * Free software: MIT license
        * Documentation: https://gnt.readthedocs.io.
        
        
        Tutorial
        --------
        To install::
        
            $ pip install gnt
        
        Basic command line usage
        ^^^^^^^^^^^^^^^^^^^^^^^^
        ::
        
            $ gnt "https://raw.githubusercontent.com/PeterDeWeirdt/bigpapi/master/data/processed/bigpapi_lfcs.csv" example_output --control CD81 --control "HPRT intron"
        
        
        Basic python usage
        ^^^^^^^^^^^^^^^^^^
        ::
        
            import gnt
            import pandas as pd
            lfcs = pd.read_csv('https://raw.githubusercontent.com/PeterDeWeirdt/bigpapi/master/data/processed/bigpapi_lfcs.csv')
            guide_residuals, model_info = gnt.get_guide_residuals(lfcs, ['CD81', 'HPRT intron'], scale=True)
            gene_scores = gnt.get_gene_residuals(guide_residuals, 'scaled_residual_z')
        
        
        TODO
        ----
        
        Credits
        -------
        
        This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
        
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
        
        
        =======
        History
        =======
        
        0.1.0 (2020-06-29)
        ------------------
        
        * First release on PyPI.
        
        0.1.1 (2020-07-09)
        ------------------
        
        * Automated release
        
        0.1.2 (2020-07-09)
        ------------------
        
        * Travis bug fix
        
        0.2.0 (2020-07-13)
        ------------------
        
        * Add columns to guide and gene output for base LFC of pairs
        * Check inputs, removing guides without the right number of pairs or control pairs
        
        
        0.2.1 (2020-07-13)
        ------------------
        
        * Update basic usage notebook
        
        0.2.2 (2020-07-15)
        ------------------
        
        * Aggregate guide scores that are in data multiple times in different orientations
        
        0.2.3 (2020-07-15)
        ------------------
        
        * Deduplicate repeat guide pairs in anchor df
        
        0.2.4 (2020-07-22)
        ------------------
        
        * Add model coefficients to guide residual ouput
        * Update delta-LFC functions
        
        0.2.5 (2020-07-27)
        ------------------
        
        * Add base LFC to dLFC output
        
        0.3.0 (2020-08-10)
        ------------------
        
        * Added spline, fixed slope and quadratic models for calculating guide residuals
        * Combined z-scores by square root of sample size rather than re-calculating z-scores
        
        0.3.1 (2020-08-10)
        ------------------
        * Centered spline for interpretable intercept
        
Keywords: gnt
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.7
