GNATpy

Welcome to GNATpy, the Gene Network rAnk enTropy python package! This package includes several methods for analyzing the rank entropy of a gene network between two different groups of samples.

Usage

GNATpy can be installed from PyPI with

pip install gnatpy

See the documentation for more information

Licensing

The original code for GNATpy is licensed under an MIT license, see the LICENSE file for more information.

The code for calculating the Kendall-Tau coefficient in the src/gnatpy/statistical_utils.py file is modified from SciPy, licensed under a BSD-3-Clause license (which is reproduced in the LICENSE file), and had a copyright disclaimer that is reproduced in the statistical_utils.py file.

The empirical p-value calculation uses code modified code from SciPy's stats module (licensed under the BSD-3-Clause, see above) for estimating the empirical p-value in line with Phipson, B., & Smyth, G. K. (2010).

The GNATpy logo is licensed under a CC0 license.

References

DIRAC

• Eddy, J. A., Hood, L., Price, N. D., & Geman, D. (2010). Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC). PLoS Computational Biology, 6(5), e1000792. https://doi.org/10.1371/journal.pcbi.1000792