semvec/pypi-packages huggingface dataset:
gnt 0.3.2
Python packcage for caidentifying Genetic iNTeractions from combinatorial screening data.
License: MIT license
Requires Python: >=3.7
Keywords: gnt

===
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

0.3.2 (2020-08-19)
------------------
* Added argument for degrees of freedom of spline