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 (Lead / Corresponding author)

Research output: Contribution to journalArticle

7 Citations (Scopus)
196 Downloads (Pure)

Abstract

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.
Original languageEnglish
Pages (from-to)3308-3310
Number of pages3
JournalBioinformatics
Volume33
Issue number20
Early online date26 Jun 2017
DOIs
Publication statusPublished - 15 Oct 2017

Keywords

  • Alternative splicing
  • Transcriptomics
  • Data analysis
  • Next-generation sequencing
  • Visualization

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    Student Theses

    Computational analysis and method development for high throughput transcriptomics and transcriptional regulatory inference in plants

    Author: Guo, W., 2018

    Supervisor: Zhang, R. (Supervisor), Brown, J. (Supervisor), Waugh, R. (Supervisor) & Lin, P. (Supervisor)

    Student thesis: Doctoral ThesisDoctor of Philosophy

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