CNAsim
CNAsim is a software package for improved simulation of single-cell copy number alteration (CNA) data from tumors. CNAsim can be used to generate copy number profiles with noise patterns that mimic those of single-cell CNA detection algorithms, and to generate DNA-seq data for sampled cells. It offers significantly improved scalability, a high degree of customizability, and improved biological realism of simulated data. Technical details appear in the paper cited below.
CNAsim is written in Python and runs reliably on versions 3.7 – 3.10. CNAsim was implemented by Samson Weiner and is available open source under GNU GPL from the GitHub link posted below. Detailed installation and usage instructions also appear in the same GitHub repository. While most users will be able to download and install CNAsim from the GitHub repository, for convenience, standalone precompiled executables for Mac and Linux operating systems are also available below.
- Source code and usage instructions on GitHub: https://github.com/samsonweiner/CNAsim
- Standalone precompiled executables for Mac and Linux: CNAsim_Mac.zip CNAsim_Linux.zip
This software can be cited as follows:
- CNAsim: Improved simulation of single-cell copy number profiles and DNA-seq data from tumors
Samson Weiner, Mukul S. Bansal
Bioinformatics, 39(7), btad434, 2023
Funding: Development of the software resource(s) available from this webpage was funded in part by U.S. National Science Foundation award IIS 2212511.
Contact: Please feel free to contact Samson Weiner (samson.weiner@uconn.edu) or Mukul Bansal (mukul.bansal@uconn.edu) if you have any questions, concerns, or suggestions.