pulseTD: RNA life cycle dynamics analysis based on pulse model of 4sU-seq time course sequencing data
2020
Xin Wang | Siyu He | Jian Li | Jun Wang | Chengyi Wang | Mingwei Wang | Danni He | Xingfeng Lv | Qiuyan Zhong | Hongjiu Wang | Zhenzhen Wang
The life cycle of intracellular RNA mainly involves transcriptional production, splicing maturation and degradation processes. Their dynamic changes are termed as RNA life cycle dynamics (RLCD). It is still challenging for the accurate and robust identification of RLCD under unknow the functional form of RLCD. By using the pulse model, we developed an R package named pulseTD to identify RLCD by integrating 4sU-seq and RNA-seq data, and it provides flexible functions to capture continuous changes in RCLD rates. More importantly, it also can predict the trend of RNA transcription and expression changes in future time points. The pulseTD shows better accuracy and robustness than some other methods, and it is available on the GitHub repository (https://github.com/bioWzz/pulseTD_0.2.0).
Show more [+] Less [-]Bibliographic information
This bibliographic record has been provided by Directory of Open Access Journals