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chimeraviz: a tool for visualizing chimeric RNA

SUMMARY: Advances in high-throughput RNA sequencing have enabled more efficient detection of fusion transcripts, but the technology and associated software used for fusion detection from sequencing data often yield a high false discovery rate. Good prioritization of the results is important, and thi...

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Autores principales: Lågstad, Stian, Zhao, Sen, Hoff, Andreas M, Johannessen, Bjarne, Lingjærde, Ole Christian, Skotheim, Rolf I
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870674/
https://www.ncbi.nlm.nih.gov/pubmed/28525538
http://dx.doi.org/10.1093/bioinformatics/btx329
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author Lågstad, Stian
Zhao, Sen
Hoff, Andreas M
Johannessen, Bjarne
Lingjærde, Ole Christian
Skotheim, Rolf I
author_facet Lågstad, Stian
Zhao, Sen
Hoff, Andreas M
Johannessen, Bjarne
Lingjærde, Ole Christian
Skotheim, Rolf I
author_sort Lågstad, Stian
collection PubMed
description SUMMARY: Advances in high-throughput RNA sequencing have enabled more efficient detection of fusion transcripts, but the technology and associated software used for fusion detection from sequencing data often yield a high false discovery rate. Good prioritization of the results is important, and this can be helped by a visualization framework that automatically integrates RNA data with known genomic features. Here we present chimeraviz, a Bioconductor package that automates the creation of chimeric RNA visualizations. The package supports input from nine different fusion-finder tools: deFuse, EricScript, InFusion, JAFFA, FusionCatcher, FusionMap, PRADA, SOAPfuse and STAR-FUSION. AVAILABILITY AND IMPLEMENTATION: chimeraviz is an R package available via Bioconductor (https://bioconductor.org/packages/release/bioc/html/chimeraviz.html) under Artistic-2.0. Source code and support is available at GitHub (https://github.com/stianlagstad/chimeraviz). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-58706742018-04-05 chimeraviz: a tool for visualizing chimeric RNA Lågstad, Stian Zhao, Sen Hoff, Andreas M Johannessen, Bjarne Lingjærde, Ole Christian Skotheim, Rolf I Bioinformatics Applications Notes SUMMARY: Advances in high-throughput RNA sequencing have enabled more efficient detection of fusion transcripts, but the technology and associated software used for fusion detection from sequencing data often yield a high false discovery rate. Good prioritization of the results is important, and this can be helped by a visualization framework that automatically integrates RNA data with known genomic features. Here we present chimeraviz, a Bioconductor package that automates the creation of chimeric RNA visualizations. The package supports input from nine different fusion-finder tools: deFuse, EricScript, InFusion, JAFFA, FusionCatcher, FusionMap, PRADA, SOAPfuse and STAR-FUSION. AVAILABILITY AND IMPLEMENTATION: chimeraviz is an R package available via Bioconductor (https://bioconductor.org/packages/release/bioc/html/chimeraviz.html) under Artistic-2.0. Source code and support is available at GitHub (https://github.com/stianlagstad/chimeraviz). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2017-09-15 2017-05-19 /pmc/articles/PMC5870674/ /pubmed/28525538 http://dx.doi.org/10.1093/bioinformatics/btx329 Text en © The Author 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Lågstad, Stian
Zhao, Sen
Hoff, Andreas M
Johannessen, Bjarne
Lingjærde, Ole Christian
Skotheim, Rolf I
chimeraviz: a tool for visualizing chimeric RNA
title chimeraviz: a tool for visualizing chimeric RNA
title_full chimeraviz: a tool for visualizing chimeric RNA
title_fullStr chimeraviz: a tool for visualizing chimeric RNA
title_full_unstemmed chimeraviz: a tool for visualizing chimeric RNA
title_short chimeraviz: a tool for visualizing chimeric RNA
title_sort chimeraviz: a tool for visualizing chimeric rna
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870674/
https://www.ncbi.nlm.nih.gov/pubmed/28525538
http://dx.doi.org/10.1093/bioinformatics/btx329
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