Thesis: Lymphocyte dynamics
This is the analysis for M. McCown's Honors Thesis at Brigham Young University, "Lymphocyte proteomics for monitoring long term immune system dynamics."
Publication
This thesis will be made available through the Harold B. Lee Library, lib.byu.edu, and on Scholar's Archive at scholarsarchive.byu.edu/
Repository contents
This repository contains all information, data, and code necessary to replicate the analyses in the manuscript.
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~/data - a folder that contains data files or url to data files
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load_data.py - a python script containing all code required for parsing data files and loading them into data frames.
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figure1_design.png - the image file for Figure 1, a graphic figure showing the design, that was created using BioRender.com
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figure2_venn.ipynb - a jupyter notebook that contains all code used in the venn diagram, shown in the manuscript as Figure 2, that demonstrates a strong shared protein profile.
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figure3_correlations.ipynb - a jupyter notebook containing the code used in generating Figure 3, showing correlation coefficients to illustrate the time dependent change.
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figure4_change_profile.ipynb - a jupyter notebook containing the code to make Figure 4, showing differentially expressed proteins a) between B cells at each time point and b) between B and T cells.
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data.md explains how data files in the repository relate to the supplemental tables from the manuscript
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data_descriptor.ipynb demonstrates how to use the methods in load_data.py, and describes the resulting dataframes.
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LICENSE.md
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README.md