gnt 0.3.2

Python packcage for caidentifying Genetic iNTeractions from combinatorial screening data.

gnt

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.

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