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TSIS: an R package to infer alternative splicing isoform switches for time-series data
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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860037/ https://www.ncbi.nlm.nih.gov/pubmed/29028262 http://dx.doi.org/10.1093/bioinformatics/btx411 |
_version_ | 1783307938217066496 |
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author | Guo, Wenbin Calixto, Cristiane P G Brown, John W S Zhang, Runxuan |
author_facet | Guo, Wenbin Calixto, Cristiane P G Brown, John W S Zhang, Runxuan |
author_sort | Guo, Wenbin |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-5860037 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-58600372018-03-23 TSIS: an R package to infer alternative splicing isoform switches for time-series data Guo, Wenbin Calixto, Cristiane P G Brown, John W S Zhang, Runxuan Bioinformatics Applications Notes 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. Oxford University Press 2017-10-15 2017-06-26 /pmc/articles/PMC5860037/ /pubmed/29028262 http://dx.doi.org/10.1093/bioinformatics/btx411 Text en © The Author 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ 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. |
spellingShingle | Applications Notes Guo, Wenbin Calixto, Cristiane P G Brown, John W S Zhang, Runxuan TSIS: an R package to infer alternative splicing isoform switches for time-series data |
title | TSIS: an R package to infer alternative splicing isoform switches for time-series data |
title_full | TSIS: an R package to infer alternative splicing isoform switches for time-series data |
title_fullStr | TSIS: an R package to infer alternative splicing isoform switches for time-series data |
title_full_unstemmed | TSIS: an R package to infer alternative splicing isoform switches for time-series data |
title_short | TSIS: an R package to infer alternative splicing isoform switches for time-series data |
title_sort | tsis: an r package to infer alternative splicing isoform switches for time-series data |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860037/ https://www.ncbi.nlm.nih.gov/pubmed/29028262 http://dx.doi.org/10.1093/bioinformatics/btx411 |
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