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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.
- Alternative splicing
- Data analysis
- Next-generation sequencing
Computational analysis and method development for high throughput transcriptomics and transcriptional regulatory inference in plantsAuthor: Guo, W., 2018
Student thesis: Doctoral Thesis › Doctor of Philosophy
Guo, W., Calixto, C. P. G., Brown, J. W. S., & Zhang, R. (2017). TSIS: an R package to infer alternative splicing isoform switches for time-series data. Bioinformatics, 33(20), 3308-3310. https://doi.org/10.1093/bioinformatics/btx411