Make a phylogeny using the chromatin structure information extracted from Hi-C experiments.
The code is mainly written using the Python programming language, with (currently) one script written using the Go language and the gonum library.
In order to run the pipeline, you will need:
- Python 3 (at least 3.6 for the f-string notation)
- PyToolz
- numpy
- tqdm (optional, used to display progress bar)
The documentation is available online at phylohic.rtfd.io.
The documentation is written using sphinx. If you want to build it, you will need sphinx of course, with the Read the Doc theme and the sphinx-argparse extension.
This code has been written during my work as a PhD student in a CNRS laboratory. Thus, it is licensed under the CeCILL V2.1, which very close and compatible with the GNU GPL.
The English text is in the file LICENSE and the French text is in the file
LICENSE_fr.
This code implements a method described in the third chapter of my PhD thesis. Moreover, the results presented there are obtained using the code in this repository.
If you use it, please cite my thesis:
Sylvain Pulicani.
Lien entre les réarrangements chromosomiques et la structure de la chromatine chez la Drosophile.
Autre [cs.OH]. Université Montpellier, 2018. Français.
NNT: 2018MONTS105
HAL: tel-02161932
Please note that a scientific publication is coming.