Bayesian analysis of pseudo-time resolved somatic hyper-mutations
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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
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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.

Contents
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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:
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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/

SEEK ID: https://funginet.hki-jena.de/models/22?version=1

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Created: 16th Feb 2021 at 10:42

Last used: 28th Feb 2021 at 21:01

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