Chimera: a Bioconductor package for secondary analysis of fusion products

Marco Beccuti; Matteo Carrara; Francesca Cordero; Fulvio Lazzarato; Susanna Donatelli; Francesca Nadalin; Alberto Policriti; Raffaele A Calogero

doi:10.1093/bioinformatics/btu662

Chimera: a Bioconductor package for secondary analysis of fusion products

Bioinformatics. 2014 Dec 15;30(24):3556-7. doi: 10.1093/bioinformatics/btu662. Epub 2014 Oct 6.

Authors

Marco Beccuti¹, Matteo Carrara¹, Francesca Cordero¹, Fulvio Lazzarato², Susanna Donatelli¹, Francesca Nadalin¹, Alberto Policriti¹, Raffaele A Calogero¹

Affiliations

¹ Department 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.
² Department 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 Department 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.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Gene Fusion*
Molecular Sequence Annotation
Software*