Dataset Information

Chimeraviz: a tool for visualizing chimeric RNA.

ABSTRACT:

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 ).

Contact

rolf.i.skotheim@rr-research.no.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Lagstad S

PROVIDER: S-EPMC5870674 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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Publications

chimeraviz: a tool for visualizing chimeric RNA.

Lågstad Stian S Zhao Sen S Hoff Andreas M AM Johannessen Bjarne B Lingjærde Ole Christian OC Skotheim Rolf I RI

Bioinformatics (Oxford, England) 20170901 18

<h4>Summary</h4>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 ...[more]

PMID: 28525538

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