TranScan software presented in the paper entitled "Translocation Detection from Hi-C data via Scan Statistics" by Anthony Cheng, Disheng Mao, Yuping Zhang, Joseph Glaz, and Zhengqing Ouyang.
The TranScan R package detects chromosome translocation events in genome-wide proximity ligation data such as Hi-C. The accompanying translocation breakpoint finder is post-processing scripts that are written in Python.
This package has been tested on the following systems:
- macOS Sierra (v 10.12.6)
- Linux: CentOS 7
The following prerequisites are required to run TranScan
- R (3.5.1)
- ggplot2 (3.1.0)
- dplyr (0.7.8)
- ggpubr (0.2.5)
- MASS (7.3-51.1)
The following prerequisites are required to run the breakpoint finder
- Python (2.7.14)
- matplotlib (2.1.0)
- numpy (1.15.2)
- seaborn (0.9.0)
For an optimized performance, consider installing OpenBLAS or ATLAS and export the following environmental variable that points to the appropriate shared object. There is an approximately 5 fold improvement in the runtime performance as compared to the default R blas implementation: libRblas.
export LD_PRELOAD=</path/to/libopenblas.so>
export LD_PRELOAD=</path/to/libatlas.so>
install.packages("devtools")
devtools::install("TranScan")
library(TranScan)
Reproducible code examples can be found in the following HTML renders of the jupyter notebooks
- Notebook01_Run_TranScan.html
The implementations written for this project is covered by the GNU General Public License, version 3.0 (GPL-3.0).