tugHall (tumor gene-Hallmark) is a cancer-cell evolution model simulator, wherein gene mutations are linked to the hallmarks of cancer, which influence tumor cell behaviors.
This is an R-based package to simulate the cancer cell evolution in the framework of the model proposed by Prof. Mamoru Kato, Head of Bioinformatics Division, Research Institute, National Cancer Center, Tokyo, JAPAN.
Iurii Nagornov (Maintainer, Author)
Munmee Dutta (Contributor)
Jo Nishino (Contributor)
Eisaku Furukawa (Contributor)
Mamoru Kato (Author)
Division of Bioinformatics, Research Institute, National Cancer Center Japan, Tokyo, Japan
All questions and requests can be sent to inagonov@ncc.go.jp or nagornov.yuri@gmail.com
The wide availability of recent cancer genomic data requires a coherent model that can sort out the relevant findings to systematically explain the clonal evolution and resultant intra-tumor heterogeneity (ITH). Here, we present a new mathematical model designed to computationally simulate the evolution of cancer cells. The model connects well-known cancer hallmarks with the specific mutational states of tumor-related genes. The cell behavior phenotypes are stochastically determined and the hallmarks interfere probabilistically with the phenotypic probabilities. In turn, the hallmark variables depend on the mutational states of tumor-related genes. Thus, it is expected our software can be used to deepen our understanding of cancer-cell evolution and generation of ITH.
Please, kindly install tugHall.3 package from source file. Firstly, download file 'tugHall.3_3.0.tar.gz' from repository to the working folder, and then:
install.packages("./tugHall.3_3.0.tar.gz", repos = NULL, type = "source")
How to use tugHall.3 and how to analyze data, kindly see vignettes in the package documentation or see code in the pipeline examples. To get pipelines please, run the function:
copy_pipelines( dir = './')
For publication, please, be kind to use next references related to tugHall software:
- Model description and first version of tugHall
Iurii S Nagornov, Mamoru Kato. tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes. Bioinformatics, V.36, N11, June 2020, pp. 3597–3599
- Clone-based version of tugHall 2.0 and 2.1 with acceleration of calculation speed
Nagornov, I., Nishino, J., Kato, M. (2020). tugHall: A Tool to Reproduce Darwinian Evolution of Cancer Cells for Simulation-Based Personalized Medicine. In: Mathematical and Computational Oncology. ISMCO 2020. Lecture Notes in Computer Science, vol 12508. Springer
- for reference of tugHall.3 package, please, cite both papers and corresponding github repository: