Developmental hematopoietic stem cell variation explains clonal hematopoiesis later in life

Citation

If you use scFMC-model in your research, please cite the Nature Communications paper here.

J Kreger, JA Mooney, D Shibata, AL MacLean (2024). Developmental hematopoietic stem cell variation explains clonal hematopoiesis later in life. Nat Commun 15, 10268 (2024). https://doi.org/10.1038/s41467-024-54711-2

The bioRxiv version is available here.

Overview

This repository contains code used in the analysis of clonal dynamics of hematopoietic stem cells. The code is written in Julia (tested on version 1.8.1) and is presented in Jupyter notebooks.

Data used in the analysis is included in the data folder and is publicly available on GEO, see Table 1 in the main text for details.

Requirements

• Julia (version 1.8.1) or newer
• Jupyter notebook

Package requirements

• Statistics.jl
• LinearAlgebra.jl
• DataStructures.jl
• StatsBase.jl
• StatsPlots.jl
• Distributions.jl
• LsqFit.jl
• Random.jl
• ColorSchemes.jl
• Plots.jl; pyplot()
• DelimitedFiles.jl
• DataFrames.jl

Project contents

• README.md : this file with information about the repository and paper
• data_processing.ipynb : Jupyter notebook containing code for basic methylation data processing.
• model_simulation.ipynb : Jupyter notebook containing code for all model simulations and figures in the paper.
• data : folder for data used in the analysis, see Table 1 in the main text for details (mz = monozygotic twins, dz = dizygotic twins, ur = unrelated individuals).
• simulation files : folder for simulation files used in the analysis (mz = monozygotic twins, dz = dizygotic twins, ur = unrelated individuals).

Acknowledgments

We would like to thank all members of the MacLean lab.

Contributors