TSIS: an R package to infer alternative splicing isoform switches for time-series data

Wenbin Guo; Cristiane P G Calixto; John W S Brown; Runxuan Zhang

doi:10.1093/bioinformatics/btx411

TSIS: an R package to infer alternative splicing isoform switches for time-series data

Bioinformatics. 2017 Oct 15;33(20):3308-3310. doi: 10.1093/bioinformatics/btx411.

Authors

Wenbin Guo^{1

2}, Cristiane P G Calixto², John W S Brown^{2

3}, Runxuan Zhang¹

Affiliations

¹ Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK.
² Plant Sciences Division, School of Life Sciences, University of Dundee, Invergowrie, Dundee, Scotland DD2 5DA, UK.
³ Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK.

Abstract

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: runxuan.zhang@hutton.ac.uk.

MeSH terms

Algorithms
Alternative Splicing*
Computational Biology / methods*
Protein Isoforms*
Software*

Substances

Protein Isoforms