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

Wenbin Guo, Cristiane P. G. Calixto, John W. S. Brown, Runxuan Zhang (Lead / Corresponding author)

Plant Sciences

Research output: Contribution to journal › Article › peer-review

27 Citations (Scopus)

251 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 language	English
Pages (from-to)	3308-3310
Number of pages	3
Journal	Bioinformatics
Volume	33
Issue number	20
Early online date	26 Jun 2017
DOIs	https://doi.org/10.1093/bioinformatics/btx411
Publication status	Published - 15 Oct 2017

Keywords

Alternative splicing
Transcriptomics
Data analysis
Next-generation sequencing
Visualization

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10.1093/bioinformatics/btx411Licence: CC BY

Final Published Version
© The Author 2017. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Final published version, 175 KBLicence: CC BY

Development of SUPPA for Alternative Splicing Analysis from RNA-Seq Data in Plants Across Multiple Conditions
Brown, J. (Investigator)
Biotechnology and Biological Sciences Research Council
1/10/16 → 14/11/17
Project: Research
Mechanisms and Function of Alternative Splicing in the Plant Circadian Clock (Joint with University of Glasgow)
Brown, J. (Investigator)
Biotechnology and Biological Sciences Research Council
1/04/13 → 30/09/16
Project: Research

Computational analysis and method development for high throughput transcriptomics and transcriptional regulatory inference in plants
Guo, W. (Author), Zhang, R. (Supervisor), Brown, J. (Supervisor), Waugh, R. (Supervisor) & Lin, P. (Supervisor), 2018
Student thesis: Doctoral Thesis › Doctor of Philosophy

Cite this

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

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.",

keywords = "Alternative splicing, Transcriptomics, Data analysis, Next-generation sequencing, Visualization",

author = "Wenbin Guo and Calixto, {Cristiane P. G.} and Brown, {John W. S.} and Runxuan Zhang",

note = "Funding: BBSRC (SS/K006568/1); Scottish Government Rural and Environment Science and Analytical Services (RESAS).",

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doi = "10.1093/bioinformatics/btx411",

language = "English",

volume = "33",

pages = "3308--3310",

journal = "Bioinformatics",

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T2 - an R package to infer alternative splicing isoform switches for time-series data

AU - Guo, Wenbin

AU - Calixto, Cristiane P. G.

AU - Brown, John W. S.

AU - Zhang, Runxuan

N1 - Funding: BBSRC (SS/K006568/1); Scottish Government Rural and Environment Science and Analytical Services (RESAS).

PY - 2017/10/15

Y1 - 2017/10/15

N2 - 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.

AB - 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.

KW - Alternative splicing

KW - Transcriptomics

KW - Data analysis

KW - Next-generation sequencing

KW - Visualization

U2 - 10.1093/bioinformatics/btx411

DO - 10.1093/bioinformatics/btx411

M3 - Article

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SN - 1367-4803

VL - 33

SP - 3308

EP - 3310

JO - Bioinformatics

JF - Bioinformatics

IS - 20

ER -

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

Abstract

Keywords

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Projects

Development of SUPPA for Alternative Splicing Analysis from RNA-Seq Data in Plants Across Multiple Conditions

Mechanisms and Function of Alternative Splicing in the Plant Circadian Clock (Joint with University of Glasgow)

Student theses

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

Cite this