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
5 maintainers
Metadata
5 maintainers
Release files for gnt 0.3.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
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| gnt-0.3.2.tar.gz | 19.2 kB | Details |
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| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| gnt-0.3.2-py2.py3-none-any.whl | Python 2, Python 3 | none | any | Details |
Total release size: 29.6 kB
Release files / gnt-0.3.2.tar.gz
| Download URL | gnt-0.3.2.tar.gz |
|---|---|
| Size | 19.2 kB |
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Release files / gnt-0.3.2-py2.py3-none-any.whl
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| Tags | Python 2 Python 3 |
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