Bayesian analysis of pseudo-time resolved somatic hyper-mutations

Code for Bayesian analysis of pseudo-time resolved somatic hyper-mutations. Hirth et al., "Regulation of the germinal center reaction and somatic hypermutation dynamics by homologus recombination", Jounal of Immunology. 9, 2019, ji1900483; DOI: https://doi.org/10.4049/jimmunol.1900483

README

This package contains code and data that calulates and tests differences in realative mutation frequancy between Control and brca mutatants. Full details of the study can be found in Hirth et al., "Regulation of the germinal center reaction and somatic hypermutation dynamics by homologus recombination", Jounal of Immunology. If any part of the code is used for academic purposes or publications, please cite the above mentioned paper.

pseudo_time_analysis.py: Script for running the Bayesian analysis of realative mutation frequancy. The script produces Figures 5c and supplementary Figure 3. mutation_log_vs2.csv Comma separated file containing the numbers and types of mutations of the sequences. README: What you currently have open. LICENCE: Licencing details of this software (BSD License 3.0).

Requirements:

Python 2.7+: Code is developed and tested using Python 2.7.13 :: Anaconda custom numpy: Tested on numpy 1.11. http://www.numpy.org/ matplotlib: Tested on matplotlib 1.5.1. http://matplotlib.org/ scipy: Tested on scipy 0.18.1. https://www.scipy.org/ pandas: Tested on pandas 0.18.1. http://pandas.pydata.org/ seaborn: Tested on seaborn 0.7.1. https://seaborn.pydata.org/ scikit-learn: Tested on sklearn 0.17. http://scikit-learn.org/