TSIS：一个用于推断时间序列数据中可变剪接异构体切换的 R 包。
TSIS: an R package to infer alternative splicing isoform switches for time-series data.
机构信息
Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK.
Plant Sciences Division, School of Life Sciences, University of Dundee, Invergowrie, Dundee, Scotland DD2 5DA, UK.
出版信息
Bioinformatics. 2017 Oct 15;33(20):3308-3310. doi: 10.1093/bioinformatics/btx411.
SUMMARY
An alternative splicing isoform switch is where a pair of transcript isoforms reverse their relative expression abundances in response to external or internal stimuli. Although computational methods are available to study differential alternative splicing, few tools for detection of isoform switches exist and these are based on pairwise comparisons. Here, we provide the TSIS R package, which is the first tool for detecting significant transcript isoform switches in time-series data. The main steps of TSIS are to search for the isoform switch points in the time-series, characterize the switches and filter the results with user input parameters. All the functions are integrated into a Shiny App for ease of implementation of the analysis.
AVAILABILITY AND IMPLEMENTATION
The TSIS package is available on GitHub: https://github.com/wyguo/TSIS.
CONTACT
摘要
可变剪接异构体转换是指一对转录本异构体在对外界或内部刺激的反应中，其相对表达丰度发生逆转的现象。虽然有计算方法可用于研究差异可变剪接，但用于检测异构体转换的工具很少，且这些工具都是基于两两比较的。在这里，我们提供了 TSIS R 包，这是第一个用于检测时间序列数据中显著转录本异构体转换的工具。TSIS 的主要步骤包括在时间序列中搜索异构体转换点、对转换进行特征描述，并使用用户输入的参数对结果进行过滤。所有功能都集成到一个 Shiny App 中，以便于分析的实现。
可用性和实现
TSIS 包可在 GitHub 上获得：https://github.com/wyguo/TSIS。
联系人
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