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SigWinR; the SigWin-detector updated and ported to R
Wim C de Leeuw1, Han Rauwerda, Márcia A Inda
1MicroArray Department & Integrative Bioinformatics Unit, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands. w.c.deleeuw@uva.nl
The SigWinR package makes the SigWin-detector tool accessible on desktop computers, enhancing its usability for genomic sequence analysis. This R package improves upon the original grid-based tool with new features and better performance.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- The SigWin-detector tool identifies enriched genomic windows in sequences efficiently.
- Its grid-based nature limited accessibility to researchers with grid infrastructure.
Purpose of the Study:
- To develop the SigWinR package, porting the SigWin-detector to the R environment for broader accessibility.
- To enhance the tool's algorithm and functionality based on user feedback.
Main Methods:
- Rewriting the SigWin-detector as an R package (SigWinR) for cross-platform desktop use.
- Implementing algorithm improvements including enhanced visualizations for Ridgeograms and enriched/depleted regions.
- Adding functionality for circular sequence analysis and identification of regions of co-altered gene expression (ROCAGEs).
- Adapting the algorithm for non-regularly sampled data and analysis of windows with an even number of elements.
Main Results:
- SigWinR provides desktop accessibility to the SigWin-detector for a wider scientific audience.
- New visualizations aid in interpreting sequence data and identifying significant regions.
- The package supports analysis of circular and non-regularly sampled genomic data.
- Successful application in identifying regions of co-altered gene expression (ROCAGEs).
Conclusions:
- Porting the SigWin-detector to R as SigWinR significantly increases its accessibility for scientists.
- Algorithmic and functional improvements enhance the tool's utility and performance.
- SigWinR empowers researchers without grid access to perform advanced genomic sequence analysis.
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