This repository contains the code used to generate figures for our latest article The Nexus of Nuclear Envelope Dynamics, Circular Economy and Cancer Cell Pathophysiology at the Danish Cancer Institute. The code utilizes various R packages, including networkD3, umap, tidymodels for SVM-RBF, and plotly and ggplot2 for visualizing big datasets.
Make sure you have R and RStudio installed on your machine. You can install the required R packages easier using a package manager, such as pacman.
Clone this repository to your local machine and use the supplementary data or your own data to conduct the data analysis.
- Functional investigation using string.db
- Network generation using networkD3
- TCGA PANCAN expression analysis using UMAP
- SVM-RBF AI model for classification using tidymodels
- Iteration through datasets with coordinated data removal based on reactome knowledgebase to identify outlier specifc gene sets
This project is licensed under the GNU General Public License v3.0 - see the LICENSE.md file for details.
A big thank you goes to Joanna Maria Merchut-Maya for proofreading the manuscript. Most importantly, I thank my supervisors, Apolinar Maya-Mendoza and Jiri Bartek, for their support.