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Chimera: a Bioconductor package for secondary analysis of fusion products
Marco Beccuti1, Matteo Carrara1, Francesca Cordero1
1Department of Computer Sciences, University of Torino, C.so Svizzera 185, 10149 Torino, Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126 Torino, Department of Translational Medicine, University of Piemonte Orientale Avogadro, Novara, Unit of Cancer Epidemiology, Department of Medical Sciences, University of Turin, Turin, Department of Computational and Quantitative Biology, UMR 7238 CNRS - Université Pierre et Marie Curie, Paris, France and Department of Mathematics and Computer Science, University of Udine, Italy.
Summary:
Chimera is a Bioconductor package that organizes, annotates, analyses and validates fusions reported by different fusion detection tools; current implementation can deal with output from bellerophontes, chimeraScan, deFuse, fusionCatcher, FusionFinder, FusionHunter, FusionMap, mapSplice, Rsubread, tophat-fusion and STAR. The core of Chimera is a fusion data structure that can store fusion events detected with any of the aforementioned tools. Fusions are then easily manipulated with standard R functions or through the set of functionalities specifically developed in Chimera with the aim of supporting the user in managing fusions and discriminating false-positive results.
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