B Software tools

B.1 Python

Below is the main list of packages used for Chapter 1

• Python.⁵⁰

• dask.⁵¹

• ipython.⁵²

• matplotlib.⁵³

• napari.⁵⁴

• networkx.⁵⁵

• numpy.⁵⁶

• pandas.⁵⁷

• pickle.⁵⁸

• scikit-image.⁵⁹

• shapely.⁶⁰

B.2 R

Below is the main list of packages used for Chapter 2 as well for the reproducibility of this undergraduate research project.

• base.⁶¹
• bookdown.⁶²
• embed.⁶³
• fs.⁶⁴
• GGally.⁶⁵
• ggdist.⁶⁶
• ggpubr.⁶⁷
• here.⁶⁸
• janitor.⁶⁹
• knitr.⁷⁰
• patchwork.⁷¹
• plotly.⁷²
• renv.⁷³
• rmarkdown.⁷⁴
• sessioninfo.⁷⁵
• stringr.⁷⁶
• tidymodels.⁷⁷
• tidytext.⁷⁸
• tidyverse.⁷⁹

B.3 Julia

Below is the main list of packages used for Chapter 3.

• Julia.⁸⁰
• DrWatson.jl.⁸¹
• DifferentialEquations.jl.⁸²
• DataFrames.jl.⁸³