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Python packcage for caidentifying Genetic iNTeractions from combinatorial screening data.

Project description

gnt Documentation Status

Python package for identifying Genetic iNTeractions from combinatorial screening data.


To install:

$ pip install gnt

Basic command line usage

$ gnt "" example_output --control CD81 --control "HPRT intron"

Basic python usage

import gnt
import pandas as pd
lfcs = pd.read_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')



This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.


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

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