This repository contains the main data processing workflows, benchmarking scripts, and supplementary code associated with the manuscript: "Delineating the copy-number substructure of metastatic tumors with CopyKit".
While the CopyKit R package is the primary software tool, this repository houses the specific scripts used for the sample processing, performance benchmarks, simulations and visualizations described in the paper.
This directory contains the scripts used to evaluate the performance of CopyKit and compare it against other single-cell copy number analysis tools.
- benchmark_accuracy: Code for generating synthetic single-cell datasets to test accuracy and resolution.
- benchmark_time: Scripts to run CopyKit alongside other methods to benchmark runtime, memory usage, and segmentation accuracy.
- downsampling: Scripts to run CopyKit alongside other methods to benchmark runtime, memory usage, and segmentation accuracy.
This directory contains the primary pipeline scripts used to process the single-cell DNA sequencing data (scDNA-seq) of the 7 tumor and 3 cell line samples. This directory also includes the scripts for statistical tests and visualizations presented in the study.
Contains definition files for building the Singularity container to run the scripts in the sample_process/ directory and reproduce the results and plots in the paper.
- Main Software Package: navinlabcode/copykit The user-friendly R package for single cell copy number analysis.
- CopyKit User Guide: navinlabcode/CopyKit-UserGuide CopyKit complete documentation for general users.
- [Depreciated/outdated]Step-by-step sample process: navinlabcode/CopyKit_paper R markdown tutorial for the tumor samples shown in the manuscript.
If you use the code or workflows in this repository, please cite the CopyKit manuscript:
Junke Wang, Darlan Conterno Minussi, Alexander Davis, Runmin Wei, Hanghui Ye, Emi Sei, Aislyn Schalck, Yun Yan, Hua-Jun Wu, Shanshan Bai, Cheng Peng, Min Hu, Anna Casasent, Alejandro Contreras, Hui Chen, David Hui, Senthil Damodaran, Mary E. Edgerton, Scott Kopetz, Bora Lim, Nicholas Navin,
Delineating the copy-number substructure of metastatic tumors with CopyKit, Molecular Cell, Volume 86, Issue 2, 2026, Pages 407-422.e6, ISSN 1097-2765, https://doi.org/10.1016/j.molcel.2025.12.026.
(https://www.sciencedirect.com/science/article/pii/S109727652501024X)
For questions regarding the code in this repository, please open an issue or contact the Navin Lab at MD Anderson Cancer Center.