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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
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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 |
Sumario: | 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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